2026-03-23T15:47:43,540 Created temporary directory: /tmp/pip-build-tracker-ghh_aicw
2026-03-23T15:47:43,541 Initialized build tracking at /tmp/pip-build-tracker-ghh_aicw
2026-03-23T15:47:43,542 Created build tracker: /tmp/pip-build-tracker-ghh_aicw
2026-03-23T15:47:43,542 Entered build tracker: /tmp/pip-build-tracker-ghh_aicw
2026-03-23T15:47:43,542 Created temporary directory: /tmp/pip-wheel-i9z1lcd6
2026-03-23T15:47:43,546 Created temporary directory: /tmp/pip-ephem-wheel-cache-c683ym5o
2026-03-23T15:47:43,619 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-23T15:47:43,622 2 location(s) to search for versions of pmx-biobb:
2026-03-23T15:47:43,622 * https://pypi.org/simple/pmx-biobb/
2026-03-23T15:47:43,622 * https://www.piwheels.org/simple/pmx-biobb/
2026-03-23T15:47:43,622 Fetching project page and analyzing links: https://pypi.org/simple/pmx-biobb/
2026-03-23T15:47:43,622 Getting page https://pypi.org/simple/pmx-biobb/
2026-03-23T15:47:43,624 Found index url https://pypi.org/simple/
2026-03-23T15:47:43,863 Fetched page https://pypi.org/simple/pmx-biobb/ as application/vnd.pypi.simple.v1+json
2026-03-23T15:47:43,871   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/ea/0e/652070bd7d0ca56047ee9da48bdce6ad248973b822b5fe7d931c07a93625/pmx_biobb-1.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,872   Link requires a different Python (3.13.5 not in: '==3.7.*'): https://files.pythonhosted.org/packages/c3/e5/f2e9751452ed944cd072d3cde0ec9523f4b3bfbde758a1b325d3d0ee42cf/pmx_biobb-1.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,873   Skipping link: 1.0.0 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/c3/e5/f2e9751452ed944cd072d3cde0ec9523f4b3bfbde758a1b325d3d0ee42cf/pmx_biobb-1.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,873   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/88/5b/2f2f6e34ed256b51485f1313f89aeb9647a2df056fad635dc6c69354a142/pmx_biobb-1.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,873   Link requires a different Python (3.13.5 not in: '==3.7.*'): https://files.pythonhosted.org/packages/44/5e/69dc9d443dcb657ec4849d483f4e759b6e40192def9d15d46fb85f2e8ba2/pmx_biobb-1.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,874   Skipping link: 1.0.1 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/44/5e/69dc9d443dcb657ec4849d483f4e759b6e40192def9d15d46fb85f2e8ba2/pmx_biobb-1.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,874   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/dc/26/88efc470b39ed04650850696ca8d4c1777e1f1788960a41b063c4f9f64cc/pmx_biobb-2.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,875   Found link https://files.pythonhosted.org/packages/32/7c/dd656cd2d785a7b9815e0ca54fb9bec35c258cdc058d9450726e65bc201c/pmx_biobb-2.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 2.0.0
2026-03-23T15:47:43,876   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/73/a2/51564515b8b81b725a8aa81b962e040e66d59ce4637be894cf02315fc403/pmx_biobb-3.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,876   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/e7/93/4fac73a6fe156e0940953662d457f0424e847a9546db1c10a7bbad5d3642/pmx_biobb-3.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,876   Found link https://files.pythonhosted.org/packages/3c/b8/7dcc8b482f02b8ff26aa1a9819fd389f9cc01087954d968e156a073ea4ac/pmx_biobb-3.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.1
2026-03-23T15:47:43,877   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/c4/2a/c00053a2535945c6900b99621be5c40437e939c64f36ea7d14e3bb5febbe/pmx_biobb-3.0.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,877   Found link https://files.pythonhosted.org/packages/8a/0b/e7b469ecf2b337e713cafe136f826f79709c9940a4d3a1eb00a669657af0/pmx_biobb-3.0.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.2
2026-03-23T15:47:43,878   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/8a/70/3744fd3fd4d13d0fcd04c50740aa9584ba6c5b7eb43e1a4dd65a7c223cf2/pmx_biobb-3.0.3-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,878   Found link https://files.pythonhosted.org/packages/6f/b2/61607c93aa5d3c34838e44ed7df748137d3b266a06a32b6d521a19ddedb4/pmx_biobb-3.0.3.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.3
2026-03-23T15:47:43,879   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/34/3e/e0a91c21ec82ca2108ec1f20c6f9fb0feb3e83b1d9277b2b521b43e77067/pmx_biobb-4.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,879   Found link https://files.pythonhosted.org/packages/d3/ee/61a98e8a9a4a1d5ab8ea32a2712cc1dfb3d7326a8404fcbd3347b28fab4d/pmx_biobb-4.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.0
2026-03-23T15:47:43,879   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/cf/d3/2cac189bd5b21c71cb79a57bf2f38121a2ecc930294758e3565302de7d21/pmx_biobb-4.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,880   Found link https://files.pythonhosted.org/packages/b9/64/0a7b31944dfae299db2a1da0949f82c4843cbc8ee4abb2f2b3f716d38640/pmx_biobb-4.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.1
2026-03-23T15:47:43,880   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/88/6d/c32f57cf60dce3b6835df798488a8e6980ca6e2865723f9e1c9551a8bff3/pmx_biobb-4.0.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,881   Found link https://files.pythonhosted.org/packages/1e/f1/377ebcaabe3ae496f4e58c434464cc6899d7a1a6287abea0ac19c9a84f38/pmx_biobb-4.0.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.2
2026-03-23T15:47:43,881   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/21/d8/92f5da41c0ccee7807122989b44711b075159e3129707c40a469a5333825/pmx_biobb-4.1.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,882   Found link https://files.pythonhosted.org/packages/de/e6/7e0419f8305191fb52c09e3f36db33fa8e37e029e6e2d0c361cb384cfefa/pmx_biobb-4.1.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.1.2
2026-03-23T15:47:43,882   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/8f/b7/67894a846ff237417e009dd532d744eff5fd675e98ccb50e27fda4c145e1/pmx_biobb-4.1.3-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,882   Found link https://files.pythonhosted.org/packages/ff/3a/d6a0cec96cc00189a683995a26e729c9d09e503129b35192923c46bd93ed/pmx_biobb-4.1.3.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.1.3
2026-03-23T15:47:43,883   Found link https://files.pythonhosted.org/packages/a8/4e/25bd821ca79c5cf26558617be7b519e15d7a160d0bb3d9b9d6e5e826975e/pmx_biobb-5.2.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.10), version: 5.2.0
2026-03-23T15:47:43,884   Found link https://files.pythonhosted.org/packages/ba/96/4bd005ce3d4c0c715be9a91cb98c0af6f871d0303415cdd3a5a79e27946f/pmx_biobb-5.2.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.10), version: 5.2.1
2026-03-23T15:47:43,884   Found link https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.9), version: 5.2.2
2026-03-23T15:47:43,885 Fetching project page and analyzing links: https://www.piwheels.org/simple/pmx-biobb/
2026-03-23T15:47:43,885 Getting page https://www.piwheels.org/simple/pmx-biobb/
2026-03-23T15:47:43,886 Found index url https://www.piwheels.org/simple/
2026-03-23T15:47:43,981 Fetched page https://www.piwheels.org/simple/pmx-biobb/ as text/html
2026-03-23T15:47:43,992   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.2-cp311-cp311-linux_armv6l.whl#sha256=f1ddfc034712fd5bf794f676e9d34b3dd905c15bc3d03a8412587dc4748ec89a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.9)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.2-cp311-cp311-linux_armv7l.whl#sha256=f1ddfc034712fd5bf794f676e9d34b3dd905c15bc3d03a8412587dc4748ec89a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.9)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.2-cp39-cp39-linux_armv6l.whl#sha256=d252b52841e2b615bf5678de4ceeec7c1de0506657ce4a5eb570f9151007376f (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.9)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.2-cp39-cp39-linux_armv7l.whl#sha256=d252b52841e2b615bf5678de4ceeec7c1de0506657ce4a5eb570f9151007376f (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.9)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp311-cp311-linux_armv6l.whl#sha256=2a0d3dadcb1b00cce1cf39fe332a083a145f0c142d06c67b49cb5f0ae09e0cac (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp311-cp311-linux_armv7l.whl#sha256=2a0d3dadcb1b00cce1cf39fe332a083a145f0c142d06c67b49cb5f0ae09e0cac (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp313-cp313-linux_armv6l.whl#sha256=90a801512df6c5c518f5664ee26983ceb1f4991b01ac289edff33dbdc5b3911d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp313-cp313-linux_armv7l.whl#sha256=90a801512df6c5c518f5664ee26983ceb1f4991b01ac289edff33dbdc5b3911d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,993   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.0-cp311-cp311-linux_armv6l.whl#sha256=674c314199bb33edcf62c2e5acef5e2852ac4be5aa1d93b4aa13b6db7b4c6674 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.0-cp311-cp311-linux_armv7l.whl#sha256=674c314199bb33edcf62c2e5acef5e2852ac4be5aa1d93b4aa13b6db7b4c6674 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp37-cp37m-linux_armv6l.whl#sha256=49e6d6e858b81a9cb06fd1e8dfb1a6813af3e81f6f471e1473a782a4063ca3eb (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp37-cp37m-linux_armv7l.whl#sha256=49e6d6e858b81a9cb06fd1e8dfb1a6813af3e81f6f471e1473a782a4063ca3eb (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp39-cp39-linux_armv6l.whl#sha256=53bd7ffc22fe4dae9200c2f72b9650e77d4ab7809ecb0219685e7429222e7b43 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp39-cp39-linux_armv7l.whl#sha256=53bd7ffc22fe4dae9200c2f72b9650e77d4ab7809ecb0219685e7429222e7b43 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp311-cp311-linux_armv6l.whl#sha256=c8756d69d71e4ca7d72f84df02cf29e97e8b7ed8f41949404774e3ba7accb428 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp311-cp311-linux_armv7l.whl#sha256=c8756d69d71e4ca7d72f84df02cf29e97e8b7ed8f41949404774e3ba7accb428 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,994   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp37-cp37m-linux_armv6l.whl#sha256=c9442c9129d171b9470330209ab7822af7bdaeaaae306c2c891597b1267bfec5 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp37-cp37m-linux_armv7l.whl#sha256=c9442c9129d171b9470330209ab7822af7bdaeaaae306c2c891597b1267bfec5 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp39-cp39-linux_armv6l.whl#sha256=5cfda4f30e6f90d0f14fdd9d401fec01a00d3b528b9cd88614bc3161a158087a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp39-cp39-linux_armv7l.whl#sha256=5cfda4f30e6f90d0f14fdd9d401fec01a00d3b528b9cd88614bc3161a158087a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp37-cp37m-linux_armv6l.whl#sha256=dff92724f2cf8b25319328fe3e99d42581794b289ae551733a6615c659395b84 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp37-cp37m-linux_armv7l.whl#sha256=dff92724f2cf8b25319328fe3e99d42581794b289ae551733a6615c659395b84 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp39-cp39-linux_armv6l.whl#sha256=47ab27371c794d3c80f75be7a95551af23c6e6a52f55acc0bf15aca71c443d0b (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp39-cp39-linux_armv7l.whl#sha256=47ab27371c794d3c80f75be7a95551af23c6e6a52f55acc0bf15aca71c443d0b (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,995   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp37-cp37m-linux_armv6l.whl#sha256=4cba66df7056ed44e240f4e96c0a53a26e29aed4edb814b23de779fbc2de2b6e (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp37-cp37m-linux_armv7l.whl#sha256=4cba66df7056ed44e240f4e96c0a53a26e29aed4edb814b23de779fbc2de2b6e (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp39-cp39-linux_armv6l.whl#sha256=bd751f2807a45f17c0e9676ccda12b6edbbebf475c170e3ec27044838f1d5b82 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp39-cp39-linux_armv7l.whl#sha256=bd751f2807a45f17c0e9676ccda12b6edbbebf475c170e3ec27044838f1d5b82 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp311-cp311-linux_armv6l.whl#sha256=b0398fae5229f8915a467bfa70ecf4855a9df4be5b25b6846c503634fd819011 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp311-cp311-linux_armv7l.whl#sha256=b0398fae5229f8915a467bfa70ecf4855a9df4be5b25b6846c503634fd819011 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp37-cp37m-linux_armv6l.whl#sha256=a27ba6f102f456ee697a94e3336dc27b59746723f1054ffdd4229bc85b007dd1 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp37-cp37m-linux_armv7l.whl#sha256=a27ba6f102f456ee697a94e3336dc27b59746723f1054ffdd4229bc85b007dd1 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,996   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp39-cp39-linux_armv6l.whl#sha256=62a965b247bcd5d3d8de872fe3c431c183e1e627d6e3103ae0fde87ff9df3ca3 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp39-cp39-linux_armv7l.whl#sha256=62a965b247bcd5d3d8de872fe3c431c183e1e627d6e3103ae0fde87ff9df3ca3 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp311-cp311-linux_armv6l.whl#sha256=bef6e7259c029c9892522e445c7f1205d39811f71f9a90bf16770566dea86f31 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp311-cp311-linux_armv7l.whl#sha256=bef6e7259c029c9892522e445c7f1205d39811f71f9a90bf16770566dea86f31 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp37-cp37m-linux_armv6l.whl#sha256=fc8fbd57b0cb8610bb25bffb894b86ccd8e7585d21e9449ddd6574a630f9b239 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp37-cp37m-linux_armv7l.whl#sha256=fc8fbd57b0cb8610bb25bffb894b86ccd8e7585d21e9449ddd6574a630f9b239 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp39-cp39-linux_armv6l.whl#sha256=40a70608dd4bf4f418963f9f6cea5d67ebf81a1a19341a6326b8df270f390f13 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp39-cp39-linux_armv7l.whl#sha256=40a70608dd4bf4f418963f9f6cea5d67ebf81a1a19341a6326b8df270f390f13 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,997   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp311-cp311-linux_armv6l.whl#sha256=7e73de5f2261d43b7ce076f78698fe893948d8d7cc9c88c7ee3def9a035a4e68 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp311-cp311-linux_armv7l.whl#sha256=7e73de5f2261d43b7ce076f78698fe893948d8d7cc9c88c7ee3def9a035a4e68 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp37-cp37m-linux_armv6l.whl#sha256=d9a0e387d6642853c6a15e0775ee01c0d16b83bc10043722ce37d48e97775ea0 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp37-cp37m-linux_armv7l.whl#sha256=d9a0e387d6642853c6a15e0775ee01c0d16b83bc10043722ce37d48e97775ea0 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp39-cp39-linux_armv6l.whl#sha256=74fd458e035071ba11d9e1399e02fc5bb4eb6423558ebf830a74400b03b09d21 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp39-cp39-linux_armv7l.whl#sha256=74fd458e035071ba11d9e1399e02fc5bb4eb6423558ebf830a74400b03b09d21 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp37-cp37m-linux_armv6l.whl#sha256=07b4c88db1007c2b4048164c399202c430d8a7a8cc06ba72b508c989771d479d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp37-cp37m-linux_armv7l.whl#sha256=07b4c88db1007c2b4048164c399202c430d8a7a8cc06ba72b508c989771d479d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp39-cp39-linux_armv6l.whl#sha256=ee00c4200b2d58c9f38a7fd4e90bf138cd1a944485cce1bdbcb00cff45c8a842 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,998   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp39-cp39-linux_armv7l.whl#sha256=ee00c4200b2d58c9f38a7fd4e90bf138cd1a944485cce1bdbcb00cff45c8a842 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp311-cp311-linux_armv6l.whl#sha256=c2f9b6cb2cb584c68d74d0ee760d79c627644692dc8371d1189026b09a9dc068 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp311-cp311-linux_armv7l.whl#sha256=c2f9b6cb2cb584c68d74d0ee760d79c627644692dc8371d1189026b09a9dc068 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp37-cp37m-linux_armv6l.whl#sha256=7ed553f6de880f8fb39de2e8b4d6ea35ed8208bf52b08e62d1bcabe12bce2581 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp37-cp37m-linux_armv7l.whl#sha256=7ed553f6de880f8fb39de2e8b4d6ea35ed8208bf52b08e62d1bcabe12bce2581 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp39-cp39-linux_armv6l.whl#sha256=49cc38d8b7531ef391784e7e40fe37f1e923ef8df1e325feb77291ce2ebbf2f9 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=49cc38d8b7531ef391784e7e40fe37f1e923ef8df1e325feb77291ce2ebbf2f9 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=06669bc75e212029d4eb66faec74a5eea1198968e9440e0b77c050a0ae585625 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:43,999   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=06669bc75e212029d4eb66faec74a5eea1198968e9440e0b77c050a0ae585625 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:44,000   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=6658576cd352d7f064666a210bfcbbf197410e312cbbdba101d4f6e4f6e9f868 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:44,000   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=6658576cd352d7f064666a210bfcbbf197410e312cbbdba101d4f6e4f6e9f868 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2026-03-23T15:47:44,000 Skipping link: not a file: https://www.piwheels.org/simple/pmx-biobb/
2026-03-23T15:47:44,000 Skipping link: not a file: https://pypi.org/simple/pmx-biobb/
2026-03-23T15:47:44,026 Given no hashes to check 1 links for project 'pmx-biobb': discarding no candidates
2026-03-23T15:47:44,027 Collecting pmx-biobb==5.2.2
2026-03-23T15:47:44,029   Created temporary directory: /tmp/pip-unpack-wv05qxwq
2026-03-23T15:47:44,188   Downloading pmx_biobb-5.2.2.tar.gz (5.2 MB)
2026-03-23T15:47:47,743   Added pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-ghh_aicw'
2026-03-23T15:47:47,746   Running setup.py (path:/tmp/pip-wheel-i9z1lcd6/pmx-biobb_4acc7032d53547218e93c201d7f3b479/setup.py) egg_info for package pmx-biobb
2026-03-23T15:47:47,747   Created temporary directory: /tmp/pip-pip-egg-info-ny9r9sr8
2026-03-23T15:47:47,747   Preparing metadata (setup.py): started
2026-03-23T15:47:47,748   Running command python setup.py egg_info
2026-03-23T15:47:48,545   /tmp/pip-wheel-i9z1lcd6/pmx-biobb_4acc7032d53547218e93c201d7f3b479/versioneer.py:564: SyntaxWarning: invalid escape sequence '\s'
2026-03-23T15:47:48,545     mo = re.search(r'=\s*"(.*)"', line)
2026-03-23T15:47:48,888   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require'
2026-03-23T15:47:48,888     warnings.warn(msg)
2026-03-23T15:47:49,483   running egg_info
2026-03-23T15:47:49,558   creating /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info
2026-03-23T15:47:49,559   writing /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/PKG-INFO
2026-03-23T15:47:49,562   writing dependency_links to /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/dependency_links.txt
2026-03-23T15:47:49,564   writing entry points to /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/entry_points.txt
2026-03-23T15:47:49,565   writing requirements to /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/requires.txt
2026-03-23T15:47:49,567   writing top-level names to /tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/top_level.txt
2026-03-23T15:47:49,568   writing manifest file '/tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/SOURCES.txt'
2026-03-23T15:47:49,796   reading manifest file '/tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/SOURCES.txt'
2026-03-23T15:47:49,798   reading manifest template 'MANIFEST.in'
2026-03-23T15:47:50,237   adding license file 'LICENSE'
2026-03-23T15:47:50,251   writing manifest file '/tmp/pip-pip-egg-info-ny9r9sr8/pmx_biobb.egg-info/SOURCES.txt'
2026-03-23T15:47:50,368   Preparing metadata (setup.py): finished with status 'done'
2026-03-23T15:47:50,374   Source in /tmp/pip-wheel-i9z1lcd6/pmx-biobb_4acc7032d53547218e93c201d7f3b479 has version 5.2.2, which satisfies requirement pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz
2026-03-23T15:47:50,375   Removed pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-ghh_aicw'
2026-03-23T15:47:50,381 Created temporary directory: /tmp/pip-unpack-r2s90jdd
2026-03-23T15:47:50,381 Created temporary directory: /tmp/pip-unpack-a6ue55qh
2026-03-23T15:47:50,381 Building wheels for collected packages: pmx-biobb
2026-03-23T15:47:50,385   Created temporary directory: /tmp/pip-wheel-yjvomn9g
2026-03-23T15:47:50,386   DEPRECATION: Building 'pmx-biobb' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pmx-biobb'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2026-03-23T15:47:50,387   Building wheel for pmx-biobb (setup.py): started
2026-03-23T15:47:50,388   Destination directory: /tmp/pip-wheel-yjvomn9g
2026-03-23T15:47:50,388   Running command python setup.py bdist_wheel
2026-03-23T15:47:51,107   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require'
2026-03-23T15:47:51,107     warnings.warn(msg)
2026-03-23T15:47:51,499   running bdist_wheel
2026-03-23T15:47:51,875   running build
2026-03-23T15:47:51,875   running build_py
2026-03-23T15:47:51,880   creating build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,882   copying src/pmx/AbsRestraints.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,885   copying src/pmx/summary.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,888   copying src/pmx/__init__.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,890   copying src/pmx/parser.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,893   copying src/pmx/utils.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,896   copying src/pmx/ndx.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,900   copying src/pmx/mutdb.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,902   copying src/pmx/atomselection.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,905   copying src/pmx/xtc.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,907   copying src/pmx/model.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,910   copying src/pmx/resselection.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,913   copying src/pmx/gmx.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,915   copying src/pmx/alchemy.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,920   copying src/pmx/geometry.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,922   copying src/pmx/builder.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,925   copying src/pmx/forcefield.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,932   copying src/pmx/estimators.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,935   copying src/pmx/jobscript.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,938   copying src/pmx/rosetta.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,941   copying src/pmx/ffparser.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,944   copying src/pmx/options.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,946   copying src/pmx/xdrfile.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,949   copying src/pmx/_version.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,951   copying src/pmx/chain.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,954   copying src/pmx/analysis.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,957   copying src/pmx/library.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,964   copying src/pmx/rotamer.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,972   copying src/pmx/molecule.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,976   copying src/pmx/rosetta_analyze.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,979   copying src/pmx/atom.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,983   copying src/pmx/ligand_alchemy.py -> build/lib.linux-armv7l-cpython-313/pmx
2026-03-23T15:47:51,993   running egg_info
2026-03-23T15:47:52,077   writing src/pmx_biobb.egg-info/PKG-INFO
2026-03-23T15:47:52,079   writing dependency_links to src/pmx_biobb.egg-info/dependency_links.txt
2026-03-23T15:47:52,081   writing entry points to src/pmx_biobb.egg-info/entry_points.txt
2026-03-23T15:47:52,083   writing requirements to src/pmx_biobb.egg-info/requires.txt
2026-03-23T15:47:52,084   writing top-level names to src/pmx_biobb.egg-info/top_level.txt
2026-03-23T15:47:52,168   reading manifest file 'src/pmx_biobb.egg-info/SOURCES.txt'
2026-03-23T15:47:52,187   reading manifest template 'MANIFEST.in'
2026-03-23T15:47:52,203   adding license file 'LICENSE'
2026-03-23T15:47:52,220   writing manifest file 'src/pmx_biobb.egg-info/SOURCES.txt'
2026-03-23T15:47:52,230   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.data' is absent from the `packages` configuration.
2026-03-23T15:47:52,230   !!

2026-03-23T15:47:52,231           ********************************************************************************
2026-03-23T15:47:52,231           ############################
2026-03-23T15:47:52,231           # Package would be ignored #
2026-03-23T15:47:52,231           ############################
2026-03-23T15:47:52,231           Python recognizes 'pmx.data' as an importable package[^1],
2026-03-23T15:47:52,231           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,231           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,231           package, please make sure that 'pmx.data' is explicitly added
2026-03-23T15:47:52,232           to the `packages` configuration field.

2026-03-23T15:47:52,232           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,232           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,232           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,232           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,232           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,232           If you don't want 'pmx.data' to be distributed and are
2026-03-23T15:47:52,233           already explicitly excluding 'pmx.data' via
2026-03-23T15:47:52,233           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,233           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,233           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,233           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,233           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,233           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,234                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,234                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,234                 directory, all directories are treated like packages.
2026-03-23T15:47:52,234           ********************************************************************************

2026-03-23T15:47:52,234   !!
2026-03-23T15:47:52,234     check.warn(importable)
2026-03-23T15:47:52,234   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.data.mutff' is absent from the `packages` configuration.
2026-03-23T15:47:52,234   !!

2026-03-23T15:47:52,235           ********************************************************************************
2026-03-23T15:47:52,235           ############################
2026-03-23T15:47:52,235           # Package would be ignored #
2026-03-23T15:47:52,235           ############################
2026-03-23T15:47:52,235           Python recognizes 'pmx.data.mutff' as an importable package[^1],
2026-03-23T15:47:52,235           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,235           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,235           package, please make sure that 'pmx.data.mutff' is explicitly added
2026-03-23T15:47:52,235           to the `packages` configuration field.

2026-03-23T15:47:52,236           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,236           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,236           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,236           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,236           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,236           If you don't want 'pmx.data.mutff' to be distributed and are
2026-03-23T15:47:52,236           already explicitly excluding 'pmx.data.mutff' via
2026-03-23T15:47:52,237           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,237           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,237           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,237           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,237           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,237           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,237                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,238                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,238                 directory, all directories are treated like packages.
2026-03-23T15:47:52,238           ********************************************************************************

2026-03-23T15:47:52,238   !!
2026-03-23T15:47:52,238     check.warn(importable)
2026-03-23T15:47:52,241   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.extensions.pmx' is absent from the `packages` configuration.
2026-03-23T15:47:52,241   !!

2026-03-23T15:47:52,241           ********************************************************************************
2026-03-23T15:47:52,242           ############################
2026-03-23T15:47:52,242           # Package would be ignored #
2026-03-23T15:47:52,242           ############################
2026-03-23T15:47:52,242           Python recognizes 'pmx.extensions.pmx' as an importable package[^1],
2026-03-23T15:47:52,242           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,242           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,242           package, please make sure that 'pmx.extensions.pmx' is explicitly added
2026-03-23T15:47:52,242           to the `packages` configuration field.

2026-03-23T15:47:52,243           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,243           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,243           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,243           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,243           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,243           If you don't want 'pmx.extensions.pmx' to be distributed and are
2026-03-23T15:47:52,243           already explicitly excluding 'pmx.extensions.pmx' via
2026-03-23T15:47:52,243           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,244           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,244           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,244           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,244           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,244           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,244                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,244                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,245                 directory, all directories are treated like packages.
2026-03-23T15:47:52,245           ********************************************************************************

2026-03-23T15:47:52,245   !!
2026-03-23T15:47:52,245     check.warn(importable)
2026-03-23T15:47:52,245   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.extensions.xdr' is absent from the `packages` configuration.
2026-03-23T15:47:52,245   !!

2026-03-23T15:47:52,246           ********************************************************************************
2026-03-23T15:47:52,246           ############################
2026-03-23T15:47:52,246           # Package would be ignored #
2026-03-23T15:47:52,246           ############################
2026-03-23T15:47:52,246           Python recognizes 'pmx.extensions.xdr' as an importable package[^1],
2026-03-23T15:47:52,246           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,246           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,246           package, please make sure that 'pmx.extensions.xdr' is explicitly added
2026-03-23T15:47:52,246           to the `packages` configuration field.

2026-03-23T15:47:52,247           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,247           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,247           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,247           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,247           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,247           If you don't want 'pmx.extensions.xdr' to be distributed and are
2026-03-23T15:47:52,247           already explicitly excluding 'pmx.extensions.xdr' via
2026-03-23T15:47:52,247           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,248           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,248           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,248           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,248           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,248           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,248                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,248                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,248                 directory, all directories are treated like packages.
2026-03-23T15:47:52,249           ********************************************************************************

2026-03-23T15:47:52,249   !!
2026-03-23T15:47:52,249     check.warn(importable)
2026-03-23T15:47:52,249   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.rosetta_example' is absent from the `packages` configuration.
2026-03-23T15:47:52,249   !!

2026-03-23T15:47:52,249           ********************************************************************************
2026-03-23T15:47:52,249           ############################
2026-03-23T15:47:52,249           # Package would be ignored #
2026-03-23T15:47:52,249           ############################
2026-03-23T15:47:52,250           Python recognizes 'pmx.rosetta_example' as an importable package[^1],
2026-03-23T15:47:52,250           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,250           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,250           package, please make sure that 'pmx.rosetta_example' is explicitly added
2026-03-23T15:47:52,250           to the `packages` configuration field.

2026-03-23T15:47:52,250           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,250           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,250           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,250           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,251           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,251           If you don't want 'pmx.rosetta_example' to be distributed and are
2026-03-23T15:47:52,251           already explicitly excluding 'pmx.rosetta_example' via
2026-03-23T15:47:52,251           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,251           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,251           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,251           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,252           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,252           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,252                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,252                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,252                 directory, all directories are treated like packages.
2026-03-23T15:47:52,252           ********************************************************************************

2026-03-23T15:47:52,252   !!
2026-03-23T15:47:52,252     check.warn(importable)
2026-03-23T15:47:52,252   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.scripts' is absent from the `packages` configuration.
2026-03-23T15:47:52,253   !!

2026-03-23T15:47:52,253           ********************************************************************************
2026-03-23T15:47:52,253           ############################
2026-03-23T15:47:52,253           # Package would be ignored #
2026-03-23T15:47:52,253           ############################
2026-03-23T15:47:52,253           Python recognizes 'pmx.scripts' as an importable package[^1],
2026-03-23T15:47:52,253           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,253           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,253           package, please make sure that 'pmx.scripts' is explicitly added
2026-03-23T15:47:52,254           to the `packages` configuration field.

2026-03-23T15:47:52,254           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,254           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,254           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,254           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,254           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,254           If you don't want 'pmx.scripts' to be distributed and are
2026-03-23T15:47:52,254           already explicitly excluding 'pmx.scripts' via
2026-03-23T15:47:52,255           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,255           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,255           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,255           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,255           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,255           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,256                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,256                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,256                 directory, all directories are treated like packages.
2026-03-23T15:47:52,256           ********************************************************************************

2026-03-23T15:47:52,256   !!
2026-03-23T15:47:52,256     check.warn(importable)
2026-03-23T15:47:52,256   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pmx.scripts.icolos_entrypoints' is absent from the `packages` configuration.
2026-03-23T15:47:52,256   !!

2026-03-23T15:47:52,257           ********************************************************************************
2026-03-23T15:47:52,257           ############################
2026-03-23T15:47:52,257           # Package would be ignored #
2026-03-23T15:47:52,257           ############################
2026-03-23T15:47:52,257           Python recognizes 'pmx.scripts.icolos_entrypoints' as an importable package[^1],
2026-03-23T15:47:52,257           but it is absent from setuptools' `packages` configuration.

2026-03-23T15:47:52,257           This leads to an ambiguous overall configuration. If you want to distribute this
2026-03-23T15:47:52,257           package, please make sure that 'pmx.scripts.icolos_entrypoints' is explicitly added
2026-03-23T15:47:52,257           to the `packages` configuration field.

2026-03-23T15:47:52,258           Alternatively, you can also rely on setuptools' discovery methods
2026-03-23T15:47:52,258           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-03-23T15:47:52,258           instead of `find_packages(...)`/`find:`).

2026-03-23T15:47:52,258           You can read more about "package discovery" on setuptools documentation page:

2026-03-23T15:47:52,258           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-03-23T15:47:52,258           If you don't want 'pmx.scripts.icolos_entrypoints' to be distributed and are
2026-03-23T15:47:52,259           already explicitly excluding 'pmx.scripts.icolos_entrypoints' via
2026-03-23T15:47:52,260           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-03-23T15:47:52,260           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-03-23T15:47:52,260           combination with a more fine grained `package-data` configuration.

2026-03-23T15:47:52,260           You can read more about "package data files" on setuptools documentation page:

2026-03-23T15:47:52,261           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-03-23T15:47:52,261           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-03-23T15:47:52,261                 even if it does not contain any `.py` files.
2026-03-23T15:47:52,261                 On the other hand, currently there is no concept of package data
2026-03-23T15:47:52,261                 directory, all directories are treated like packages.
2026-03-23T15:47:52,261           ********************************************************************************

2026-03-23T15:47:52,262   !!
2026-03-23T15:47:52,262     check.warn(importable)
2026-03-23T15:47:52,262   creating build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,262   copying src/pmx/data/aminoacids.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,268   copying src/pmx/data/bbdep.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,844   copying src/pmx/data/blosum62_new.mat -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,846   copying src/pmx/data/bp.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,852   copying src/pmx/data/bp_amber.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,857   copying src/pmx/data/bp_charmm.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,862   copying src/pmx/data/rna.pkl -> build/lib.linux-armv7l-cpython-313/pmx/data
2026-03-23T15:47:52,866   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,867   copying src/pmx/data/mutff/atommass.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,869   copying src/pmx/data/mutff/elements.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,872   copying src/pmx/data/mutff/residuetypes.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,874   copying src/pmx/data/mutff/spc216.gro -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,878   copying src/pmx/data/mutff/specbond.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,880   copying src/pmx/data/mutff/vdwradii.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,882   copying src/pmx/data/mutff/xlateat.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff
2026-03-23T15:47:52,884   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,885   copying src/pmx/data/mutff/amber14sbmut.ff/Makefile.am -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,888   copying src/pmx/data/mutff/amber14sbmut.ff/Makefile.in -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,891   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,894   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,896   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,899   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,901   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,903   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,908   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,910   copying src/pmx/data/mutff/amber14sbmut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,913   copying src/pmx/data/mutff/amber14sbmut.ff/dna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,915   copying src/pmx/data/mutff/amber14sbmut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,917   copying src/pmx/data/mutff/amber14sbmut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,919   copying src/pmx/data/mutff/amber14sbmut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,922   copying src/pmx/data/mutff/amber14sbmut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,927   copying src/pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,929   copying src/pmx/data/mutff/amber14sbmut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,931   copying src/pmx/data/mutff/amber14sbmut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,933   copying src/pmx/data/mutff/amber14sbmut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,936   copying src/pmx/data/mutff/amber14sbmut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:52,938   copying src/pmx/data/mutff/amber14sbmut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,001   copying src/pmx/data/mutff/amber14sbmut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,029   copying src/pmx/data/mutff/amber14sbmut.ff/rna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,032   copying src/pmx/data/mutff/amber14sbmut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,034   copying src/pmx/data/mutff/amber14sbmut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,037   copying src/pmx/data/mutff/amber14sbmut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,040   copying src/pmx/data/mutff/amber14sbmut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,042   copying src/pmx/data/mutff/amber14sbmut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,044   copying src/pmx/data/mutff/amber14sbmut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,046   copying src/pmx/data/mutff/amber14sbmut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,048   copying src/pmx/data/mutff/amber14sbmut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,050   copying src/pmx/data/mutff/amber14sbmut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,052   copying src/pmx/data/mutff/amber14sbmut.ff/urea.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,054   copying src/pmx/data/mutff/amber14sbmut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:47:53,057   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,058   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,064   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,069   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,074   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,077   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,079   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,083   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,088   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,091   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,094   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,097   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,123   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,127   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,129   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,131   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,134   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,137   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,141   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,144   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,147   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,150   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,152   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,155   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,158   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,168   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,174   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,177   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,181   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,183   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,185   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,187   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,191   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,193   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,196   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,198   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,201   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,203   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,206   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,208   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:47:53,211   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,212   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,215   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,217   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,220   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,223   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,225   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,231   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,234   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,237   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,240   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,272   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,275   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,278   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,280   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,282   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,285   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,288   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,292   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,294   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,296   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,298   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,301   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,303   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,311   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,317   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,320   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,323   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,325   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,328   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,330   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,333   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,335   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,337   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,339   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,341   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,344   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,346   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,348   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:47:53,350   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,351   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,354   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,356   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,359   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,361   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,363   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,368   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,371   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,374   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,376   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,378   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,380   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,383   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,386   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,389   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,391   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,393   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,395   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,397   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,495   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,522   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,524   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,526   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,529   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,532   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,534   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,536   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,538   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,541   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,543   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,546   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,548   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:47:53,550   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,552   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,554   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,557   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,559   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,562   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,564   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,568   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,570   copying src/pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,578   copying src/pmx/data/mutff/charmm22star-mut.ff/cmap.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,582   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,584   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,587   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,589   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,592   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,595   copying src/pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,600   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,605   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,609   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,615   copying src/pmx/data/mutff/charmm22star-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,617   copying src/pmx/data/mutff/charmm22star-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,619   copying src/pmx/data/mutff/charmm22star-mut.ff/gb.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,622   copying src/pmx/data/mutff/charmm22star-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,624   copying src/pmx/data/mutff/charmm22star-mut.ff/lipids.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,626   copying src/pmx/data/mutff/charmm22star-mut.ff/lipids.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,629   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,631   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,679   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,703   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,705   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,708   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,710   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,712   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,715   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,718   copying src/pmx/data/mutff/charmm22star-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,720   copying src/pmx/data/mutff/charmm22star-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,723   copying src/pmx/data/mutff/charmm22star-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,725   copying src/pmx/data/mutff/charmm22star-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,728   copying src/pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,730   copying src/pmx/data/mutff/charmm22star-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,733   copying src/pmx/data/mutff/charmm22star-mut.ff/tips3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,735   copying src/pmx/data/mutff/charmm22star-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:47:53,737   creating build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,738   copying src/pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,742   copying src/pmx/data/mutff/charmm36m-mut.ff/cmap.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,746   copying src/pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,770   copying src/pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,798   copying src/pmx/data/mutff/charmm36m-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,801   copying src/pmx/data/mutff/charmm36m-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,803   copying src/pmx/data/mutff/charmm36m-mut.ff/gb.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,805   copying src/pmx/data/mutff/charmm36m-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,808   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,810   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,813   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.hdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,816   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,818   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.r2b -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,820   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,845   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.vsd -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,847   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.arn -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,849   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,898   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,921   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,930   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,935   copying src/pmx/data/mutff/charmm36m-mut.ff/nbfix.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,937   copying src/pmx/data/mutff/charmm36m-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,940   copying src/pmx/data/mutff/charmm36m-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,942   copying src/pmx/data/mutff/charmm36m-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,945   copying src/pmx/data/mutff/charmm36m-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,947   copying src/pmx/data/mutff/charmm36m-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:47:53,949   creating build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,951   copying src/pmx/extensions/pmx/Energy.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,954   copying src/pmx/extensions/pmx/Geometry.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,957   copying src/pmx/extensions/pmx/Geometry.h -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,960   copying src/pmx/extensions/pmx/cpp_test.cpp -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,963   copying src/pmx/extensions/pmx/init.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,965   copying src/pmx/extensions/pmx/pmx.h -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,968   copying src/pmx/extensions/pmx/wrap_Geometry.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx
2026-03-23T15:47:53,972   creating build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,973   copying src/pmx/extensions/xdr/trr2xtc.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,976   copying src/pmx/extensions/xdr/xdrfile.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,980   copying src/pmx/extensions/xdr/xdrfile.h -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,984   copying src/pmx/extensions/xdr/xdrfile_c_test.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,988   copying src/pmx/extensions/xdr/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,991   copying src/pmx/extensions/xdr/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,993   copying src/pmx/extensions/xdr/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,996   copying src/pmx/extensions/xdr/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr
2026-03-23T15:47:53,998   creating build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:53,999   copying src/pmx/rosetta_example/README -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,002   copying src/pmx/rosetta_example/analyze.py -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,005   copying src/pmx/rosetta_example/mut.dat -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,007   copying src/pmx/rosetta_example/plot_results.ipynb -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,015   copying src/pmx/rosetta_example/prot_zn.pdb -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,029   copying src/pmx/rosetta_example/rosetta_prepare.ipynb -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,031   copying src/pmx/rosetta_example/submit_jobscripts.py -> build/lib.linux-armv7l-cpython-313/pmx/rosetta_example
2026-03-23T15:47:54,033   creating build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,034   copying src/pmx/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,036   copying src/pmx/scripts/analyze_dhdl.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,039   copying src/pmx/scripts/atomMapping.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,042   copying src/pmx/scripts/build_cyclic_top.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,045   copying src/pmx/scripts/cli.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,048   copying src/pmx/scripts/fill_cgenff_itp.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,051   copying src/pmx/scripts/fix_residue_names.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,054   copying src/pmx/scripts/gen_abs_restraints.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,057   copying src/pmx/scripts/generate_hybrid_residue.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,062   copying src/pmx/scripts/generate_hybrid_topology.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,064   copying src/pmx/scripts/hydrogen_atom_renaming.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,067   copying src/pmx/scripts/ligandHybrid.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,070   copying src/pmx/scripts/make_double_box.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,073   copying src/pmx/scripts/md_setup.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,076   copying src/pmx/scripts/mutate.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,080   copying src/pmx/scripts/parameterize_ligands.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,084   copying src/pmx/scripts/prepare_crooks_runs.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,087   copying src/pmx/scripts/repartition_mass.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,089   copying src/pmx/scripts/set_gmxlib.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,091   copying src/pmx/scripts/setup_abfe.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts
2026-03-23T15:47:54,094   creating build/lib.linux-armv7l-cpython-313/pmx/scripts/icolos_entrypoints
2026-03-23T15:47:54,095   copying src/pmx/scripts/icolos_entrypoints/__init__.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts/icolos_entrypoints
2026-03-23T15:47:54,098   copying src/pmx/scripts/icolos_entrypoints/assemble_systems.py -> build/lib.linux-armv7l-cpython-313/pmx/scripts/icolos_entrypoints
2026-03-23T15:47:54,101   UPDATING build/lib.linux-armv7l-cpython-313/pmx/_version.py
2026-03-23T15:47:54,102   set build/lib.linux-armv7l-cpython-313/pmx/_version.py to '5.2.2'
2026-03-23T15:47:54,103   running build_ext
2026-03-23T15:47:54,737   building 'pmx._pmx' extension
2026-03-23T15:47:54,739   creating build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx
2026-03-23T15:47:54,742   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.13 -c src/pmx/extensions/pmx/Energy.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/Energy.o
2026-03-23T15:47:55,988   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.13 -c src/pmx/extensions/pmx/Geometry.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/Geometry.o
2026-03-23T15:47:56,386   src/pmx/extensions/pmx/Geometry.c: In function ‘spread_atoms_on_grid’:
2026-03-23T15:47:56,386   src/pmx/extensions/pmx/Geometry.c:527:15: warning: variable ‘nz’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:47:56,386     527 |   int nx, ny, nz;
2026-03-23T15:47:56,386         |               ^~
2026-03-23T15:47:56,387   src/pmx/extensions/pmx/Geometry.c: In function ‘search_neighbors’:
2026-03-23T15:47:56,388   src/pmx/extensions/pmx/Geometry.c:586:15: warning: variable ‘nz’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:47:56,388     586 |   int nx, ny, nz;
2026-03-23T15:47:56,388         |               ^~
2026-03-23T15:47:58,277   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.13 -c src/pmx/extensions/pmx/init.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/init.o
2026-03-23T15:47:58,947   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.13 -c src/pmx/extensions/pmx/wrap_Geometry.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/wrap_Geometry.o
2026-03-23T15:48:00,649   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/Energy.o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/Geometry.o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/init.o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/pmx/wrap_Geometry.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-313/pmx/_pmx.cpython-313-arm-linux-gnueabihf.so
2026-03-23T15:48:00,798   building 'pmx._xdrio' extension
2026-03-23T15:48:00,799   creating build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr
2026-03-23T15:48:00,800   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.13 -c src/pmx/extensions/xdr/xdrfile.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile.o
2026-03-23T15:48:00,847   src/pmx/extensions/xdr/xdrfile.c:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:00,848       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:00,939   In file included from src/pmx/extensions/xdr/xdrfile.c:60:
2026-03-23T15:48:00,939   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:00,939       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:00,947   src/pmx/extensions/xdr/xdrfile.c: In function ‘sizeofint’:
2026-03-23T15:48:00,947   src/pmx/extensions/xdr/xdrfile.c:499:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,948     499 |     while (size >= num && num_of_bits < 32)
2026-03-23T15:48:00,948         |                 ^~
2026-03-23T15:48:00,948   src/pmx/extensions/xdr/xdrfile.c: In function ‘sizeofints’:
2026-03-23T15:48:00,948   src/pmx/extensions/xdr/xdrfile.c:545:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,949     545 |     while (bytes[num_of_bytes] >= num)
2026-03-23T15:48:00,949         |                                ^~
2026-03-23T15:48:00,950   src/pmx/extensions/xdr/xdrfile.c: In function ‘encodeints’:
2026-03-23T15:48:00,950   src/pmx/extensions/xdr/xdrfile.c:654:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,951     654 |     if (num_of_bits >= num_of_bytes * 8)
2026-03-23T15:48:00,951         |                     ^~
2026-03-23T15:48:00,951   src/pmx/extensions/xdr/xdrfile.c:656:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,951     656 |                 for (i = 0; i < num_of_bytes; i++)
2026-03-23T15:48:00,951         |                               ^
2026-03-23T15:48:00,952   src/pmx/extensions/xdr/xdrfile.c:664:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,952     664 |                 for (i = 0; i < num_of_bytes-1; i++)
2026-03-23T15:48:00,952         |                               ^
2026-03-23T15:48:00,953   src/pmx/extensions/xdr/xdrfile.c: In function ‘decodebits’:
2026-03-23T15:48:00,953   src/pmx/extensions/xdr/xdrfile.c:704:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,953     704 |                 if (lastbits < num_of_bits)
2026-03-23T15:48:00,954         |                              ^
2026-03-23T15:48:00,955   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2026-03-23T15:48:00,956   src/pmx/extensions/xdr/xdrfile.c:814:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,956     814 |         if(size3>xfp->buf1size)
2026-03-23T15:48:00,956         |                 ^
2026-03-23T15:48:00,958   src/pmx/extensions/xdr/xdrfile.c:866:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,958     866 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,959         |                          ^
2026-03-23T15:48:00,959   src/pmx/extensions/xdr/xdrfile.c:866:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2026-03-23T15:48:00,959     866 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,959         |                                            ^~~
2026-03-23T15:48:00,963   src/pmx/extensions/xdr/xdrfile.c:792:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:00,963     792 |         int smallnum, smaller, larger, i, is_smaller, run;
2026-03-23T15:48:00,963         |                                ^~~~~~
2026-03-23T15:48:00,963   src/pmx/extensions/xdr/xdrfile.c:789:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:00,963     789 |         int smallidx, minidx, maxidx;
2026-03-23T15:48:00,963         |                       ^~~~~~
2026-03-23T15:48:00,964   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2026-03-23T15:48:00,965   src/pmx/extensions/xdr/xdrfile.c:1010:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,965    1010 |         if(size3>xfp->buf1size)
2026-03-23T15:48:00,965         |                 ^
2026-03-23T15:48:00,971   src/pmx/extensions/xdr/xdrfile.c:1133:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,971    1133 |         while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2026-03-23T15:48:00,971         |                         ^
2026-03-23T15:48:00,972   src/pmx/extensions/xdr/xdrfile.c:1139:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,972    1139 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,972         |                          ^
2026-03-23T15:48:00,973   src/pmx/extensions/xdr/xdrfile.c:1139:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2026-03-23T15:48:00,973    1139 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,973         |                                            ^~~
2026-03-23T15:48:00,977   src/pmx/extensions/xdr/xdrfile.c:1271:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,977    1271 |         if(tmp==(unsigned int)buf2[0])
2026-03-23T15:48:00,977         |               ^~
2026-03-23T15:48:00,978   src/pmx/extensions/xdr/xdrfile.c:999:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:00,978     999 |         int errval=1;
2026-03-23T15:48:00,978         |             ^~~~~~
2026-03-23T15:48:00,979   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2026-03-23T15:48:00,980   src/pmx/extensions/xdr/xdrfile.c:1311:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,980    1311 |         if(size3>xfp->buf1size)
2026-03-23T15:48:00,980         |                 ^
2026-03-23T15:48:00,983   src/pmx/extensions/xdr/xdrfile.c:1366:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,983    1366 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,983         |                          ^
2026-03-23T15:48:00,984   src/pmx/extensions/xdr/xdrfile.c:1366:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2026-03-23T15:48:00,984    1366 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:00,984         |                                            ^~~
2026-03-23T15:48:00,988   src/pmx/extensions/xdr/xdrfile.c:1288:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:00,988    1288 |         int smallnum, smaller, larger, i, is_smaller, run;
2026-03-23T15:48:00,988         |                                ^~~~~~
2026-03-23T15:48:00,989   src/pmx/extensions/xdr/xdrfile.c:1285:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:00,989    1285 |         int smallidx, minidx, maxidx;
2026-03-23T15:48:00,989         |                       ^~~~~~
2026-03-23T15:48:00,990   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2026-03-23T15:48:00,991   src/pmx/extensions/xdr/xdrfile.c:1502:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:00,991    1502 |         if(size3>xfp->buf1size) {
2026-03-23T15:48:00,991         |                 ^
2026-03-23T15:48:00,998   src/pmx/extensions/xdr/xdrfile.c:1617:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:00,999    1617 |         while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2026-03-23T15:48:00,999         |                         ^
2026-03-23T15:48:01,000   src/pmx/extensions/xdr/xdrfile.c:1622:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2026-03-23T15:48:01,000    1622 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:01,000         |                          ^
2026-03-23T15:48:01,002   src/pmx/extensions/xdr/xdrfile.c:1622:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2026-03-23T15:48:01,002    1622 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2026-03-23T15:48:01,002         |                                            ^~~
2026-03-23T15:48:01,006   src/pmx/extensions/xdr/xdrfile.c:1732:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2026-03-23T15:48:01,006    1732 |         if(tmp==(unsigned int)buf2[0])
2026-03-23T15:48:01,006         |               ^~
2026-03-23T15:48:01,007   src/pmx/extensions/xdr/xdrfile.c:1492:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2026-03-23T15:48:01,007    1492 |         int errval=1;
2026-03-23T15:48:01,007         |             ^~~~~~
2026-03-23T15:48:03,744   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.13 -c src/pmx/extensions/xdr/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile_trr.o
2026-03-23T15:48:03,791   src/pmx/extensions/xdr/xdrfile_trr.c:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:03,791       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:03,831   In file included from src/pmx/extensions/xdr/xdrfile_trr.c:41:
2026-03-23T15:48:03,831   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:03,831       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:03,833   In file included from src/pmx/extensions/xdr/xdrfile_trr.c:42:
2026-03-23T15:48:03,833   src/pmx/extensions/xdr/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:03,833       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:03,834   src/pmx/extensions/xdr/xdrfile_trr.c: In function ‘do_trnheader’:
2026-03-23T15:48:03,834   src/pmx/extensions/xdr/xdrfile_trr.c:108:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2026-03-23T15:48:03,834     108 |         if (slen != strlen(version)+1)
2026-03-23T15:48:03,834         |                  ^~
2026-03-23T15:48:03,835   src/pmx/extensions/xdr/xdrfile_trr.c:118:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2026-03-23T15:48:03,835     118 |         if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
2026-03-23T15:48:03,835         |                                              ^~
2026-03-23T15:48:04,570   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.13 -c src/pmx/extensions/xdr/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile_xtc.o
2026-03-23T15:48:04,654   In file included from src/pmx/extensions/xdr/xdrfile_xtc.c:31:
2026-03-23T15:48:04,654   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:04,654       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:04,656   In file included from src/pmx/extensions/xdr/xdrfile_xtc.c:32:
2026-03-23T15:48:04,656   src/pmx/extensions/xdr/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
2026-03-23T15:48:04,656       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2026-03-23T15:48:04,658   src/pmx/extensions/xdr/xdrfile_xtc.c: In function ‘xtc_coord’:
2026-03-23T15:48:04,658   src/pmx/extensions/xdr/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable]
2026-03-23T15:48:04,658      66 |         int i,j,result;
2026-03-23T15:48:04,658         |               ^
2026-03-23T15:48:04,659   src/pmx/extensions/xdr/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable]
2026-03-23T15:48:04,659      66 |         int i,j,result;
2026-03-23T15:48:04,659         |             ^
2026-03-23T15:48:04,779   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile.o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile_trr.o build/temp.linux-armv7l-cpython-313/src/pmx/extensions/xdr/xdrfile_xtc.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-313/pmx/_xdrio.cpython-313-arm-linux-gnueabihf.so
2026-03-23T15:48:04,999   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2026-03-23T15:48:04,999   !!

2026-03-23T15:48:04,999           ********************************************************************************
2026-03-23T15:48:04,999           Please avoid running ``setup.py`` directly.
2026-03-23T15:48:04,999           Instead, use pypa/build, pypa/installer or other
2026-03-23T15:48:04,999           standards-based tools.

2026-03-23T15:48:05,000           This deprecation is overdue, please update your project and remove deprecated
2026-03-23T15:48:05,000           calls to avoid build errors in the future.

2026-03-23T15:48:05,000           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2026-03-23T15:48:05,000           ********************************************************************************

2026-03-23T15:48:05,000   !!
2026-03-23T15:48:05,000     self.initialize_options()
2026-03-23T15:48:05,075   installing to build/bdist.linux-armv7l/wheel
2026-03-23T15:48:05,075   running install
2026-03-23T15:48:05,097   running install_lib
2026-03-23T15:48:05,173   creating build/bdist.linux-armv7l/wheel
2026-03-23T15:48:05,176   creating build/bdist.linux-armv7l/wheel/pmx
2026-03-23T15:48:05,177   copying build/lib.linux-armv7l-cpython-313/pmx/AbsRestraints.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,179   copying build/lib.linux-armv7l-cpython-313/pmx/summary.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,182   copying build/lib.linux-armv7l-cpython-313/pmx/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,184   copying build/lib.linux-armv7l-cpython-313/pmx/parser.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,186   copying build/lib.linux-armv7l-cpython-313/pmx/utils.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,188   copying build/lib.linux-armv7l-cpython-313/pmx/ndx.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,190   copying build/lib.linux-armv7l-cpython-313/pmx/mutdb.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,192   copying build/lib.linux-armv7l-cpython-313/pmx/_xdrio.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,199   copying build/lib.linux-armv7l-cpython-313/pmx/atomselection.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,202   creating build/bdist.linux-armv7l/wheel/pmx/rosetta_example
2026-03-23T15:48:05,203   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/submit_jobscripts.py -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,205   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/mut.dat -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,207   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/rosetta_prepare.ipynb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,209   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/plot_results.ipynb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,216   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/analyze.py -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,218   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/prot_zn.pdb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,234   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_example/README -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2026-03-23T15:48:05,235   copying build/lib.linux-armv7l-cpython-313/pmx/xtc.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,237   copying build/lib.linux-armv7l-cpython-313/pmx/model.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,240   copying build/lib.linux-armv7l-cpython-313/pmx/resselection.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,243   copying build/lib.linux-armv7l-cpython-313/pmx/gmx.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,245   copying build/lib.linux-armv7l-cpython-313/pmx/alchemy.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,249   copying build/lib.linux-armv7l-cpython-313/pmx/geometry.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,251   copying build/lib.linux-armv7l-cpython-313/pmx/builder.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,254   copying build/lib.linux-armv7l-cpython-313/pmx/forcefield.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,258   copying build/lib.linux-armv7l-cpython-313/pmx/estimators.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,262   creating build/bdist.linux-armv7l/wheel/pmx/extensions
2026-03-23T15:48:05,263   creating build/bdist.linux-armv7l/wheel/pmx/extensions/xdr
2026-03-23T15:48:05,264   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,267   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,269   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,272   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile_c_test.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,275   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,276   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,279   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/trr2xtc.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,281   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/xdr/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2026-03-23T15:48:05,283   creating build/bdist.linux-armv7l/wheel/pmx/extensions/pmx
2026-03-23T15:48:05,284   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/Geometry.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,287   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/Energy.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,290   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/pmx.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,292   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/wrap_Geometry.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,295   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/init.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,296   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/Geometry.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,299   copying build/lib.linux-armv7l-cpython-313/pmx/extensions/pmx/cpp_test.cpp -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2026-03-23T15:48:05,301   copying build/lib.linux-armv7l-cpython-313/pmx/jobscript.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,303   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:05,306   creating build/bdist.linux-armv7l/wheel/pmx/data
2026-03-23T15:48:05,307   copying build/lib.linux-armv7l-cpython-313/pmx/data/aminoacids.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,316   copying build/lib.linux-armv7l-cpython-313/pmx/data/bp_amber.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,324   copying build/lib.linux-armv7l-cpython-313/pmx/data/rna.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,327   copying build/lib.linux-armv7l-cpython-313/pmx/data/bp_charmm.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,333   copying build/lib.linux-armv7l-cpython-313/pmx/data/bbdep.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,607   copying build/lib.linux-armv7l-cpython-313/pmx/data/bp.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,612   copying build/lib.linux-armv7l-cpython-313/pmx/data/blosum62_new.mat -> build/bdist.linux-armv7l/wheel/./pmx/data
2026-03-23T15:48:05,615   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff
2026-03-23T15:48:05,616   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/spc216.gro -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:05,620   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,621   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,623   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,624   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,627   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,628   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,631   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,633   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,635   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,688   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,690   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,692   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,693   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,695   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,699   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,701   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,703   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,705   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,707   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,709   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,711   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,713   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,715   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,717   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,719   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,721   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,724   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,726   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,728   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,731   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,757   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,760   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,762   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2026-03-23T15:48:05,765   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/elements.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:05,768   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,769   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,771   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,773   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,775   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,777   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,780   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,783   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,785   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/gb.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,787   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,790   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,841   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,843   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,845   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/tips3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,847   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,849   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/mutres.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,850   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,852   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,855   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,857   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,859   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/lipids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,861   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,865   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/lipids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,868   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,870   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,873   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/cmap.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,876   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,878   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,880   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,882   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,884   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,886   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,889   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,891   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,893   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,899   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,902   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,904   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,907   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,936   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,939   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,942   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm22star-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2026-03-23T15:48:05,944   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/vdwradii.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:05,946   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/residuetypes.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:05,949   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/specbond.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:05,952   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,954   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,956   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,958   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,961   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,964   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,966   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,969   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,971   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,973   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,975   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,977   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,979   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,989   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:05,991   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,022   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,024   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,029   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,031   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,033   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,034   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,036   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,041   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,043   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,046   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,048   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,051   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,052   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,054   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,056   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,058   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,059   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,062   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,065   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,067   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,069   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,071   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,075   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,077   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,080   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2026-03-23T15:48:06,083   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,084   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,114   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,116   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,118   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,120   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,122   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,124   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/gb.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,126   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,127   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,187   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,189   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/mutres.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,191   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,198   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,201   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,205   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,207   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/cmap.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,212   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,214   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,216   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,218   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/nbfix.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,220   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,222   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,263   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,265   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,292   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,311   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2026-03-23T15:48:06,313   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/xlateat.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:06,315   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/atommass.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2026-03-23T15:48:06,319   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,320   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,322   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,324   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,327   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,329   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,331   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,333   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,335   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,396   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/Makefile.am -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,398   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,400   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,401   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,403   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,405   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,409   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,411   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,413   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,415   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,417   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,420   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,422   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,424   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/Makefile.in -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,426   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,428   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,431   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,433   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,435   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,437   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,439   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,441   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,444   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,477   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,480   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,483   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber14sbmut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2026-03-23T15:48:06,486   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,488   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,490   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,492   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,495   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,498   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,499   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,502   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,504   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,505   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,507   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,509   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,511   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,523   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,525   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,554   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,557   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,560   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,562   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,564   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,566   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,573   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,576   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,579   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,582   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,585   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,587   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,589   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,592   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,593   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,596   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,599   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,601   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,603   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,605   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,608   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,612   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,615   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,618   copying build/lib.linux-armv7l-cpython-313/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2026-03-23T15:48:06,620   copying build/lib.linux-armv7l-cpython-313/pmx/ffparser.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,624   copying build/lib.linux-armv7l-cpython-313/pmx/options.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,626   copying build/lib.linux-armv7l-cpython-313/pmx/xdrfile.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,629   copying build/lib.linux-armv7l-cpython-313/pmx/_version.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,631   copying build/lib.linux-armv7l-cpython-313/pmx/chain.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,634   copying build/lib.linux-armv7l-cpython-313/pmx/analysis.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,638   copying build/lib.linux-armv7l-cpython-313/pmx/library.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,644   copying build/lib.linux-armv7l-cpython-313/pmx/rotamer.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,646   copying build/lib.linux-armv7l-cpython-313/pmx/_pmx.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,656   creating build/bdist.linux-armv7l/wheel/pmx/scripts
2026-03-23T15:48:06,657   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/md_setup.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,660   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,662   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/fix_residue_names.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,664   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/build_cyclic_top.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,667   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/make_double_box.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,669   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/fill_cgenff_itp.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,672   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/mutate.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,675   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/repartition_mass.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,678   creating build/bdist.linux-armv7l/wheel/pmx/scripts/icolos_entrypoints
2026-03-23T15:48:06,679   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/icolos_entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts/icolos_entrypoints
2026-03-23T15:48:06,681   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/icolos_entrypoints/assemble_systems.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts/icolos_entrypoints
2026-03-23T15:48:06,683   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/generate_hybrid_residue.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,687   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/gen_abs_restraints.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,690   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/parameterize_ligands.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,693   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/hydrogen_atom_renaming.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,695   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/analyze_dhdl.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,699   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/prepare_crooks_runs.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,701   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/cli.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,703   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/ligandHybrid.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,706   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/atomMapping.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,709   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/setup_abfe.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,712   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/generate_hybrid_topology.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,714   copying build/lib.linux-armv7l-cpython-313/pmx/scripts/set_gmxlib.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2026-03-23T15:48:06,716   copying build/lib.linux-armv7l-cpython-313/pmx/molecule.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,720   copying build/lib.linux-armv7l-cpython-313/pmx/rosetta_analyze.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,722   copying build/lib.linux-armv7l-cpython-313/pmx/atom.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,727   copying build/lib.linux-armv7l-cpython-313/pmx/ligand_alchemy.py -> build/bdist.linux-armv7l/wheel/./pmx
2026-03-23T15:48:06,732   running install_egg_info
2026-03-23T15:48:06,816   Copying src/pmx_biobb.egg-info to build/bdist.linux-armv7l/wheel/./pmx_biobb-5.2.2-py3.13.egg-info
2026-03-23T15:48:06,829   running install_scripts
2026-03-23T15:48:06,897   creating build/bdist.linux-armv7l/wheel/pmx_biobb-5.2.2.dist-info/WHEEL
2026-03-23T15:48:06,900   creating '/tmp/pip-wheel-yjvomn9g/pmx_biobb-5.2.2-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-23T15:48:06,904   adding 'pmx/AbsRestraints.py'
2026-03-23T15:48:06,906   adding 'pmx/__init__.py'
2026-03-23T15:48:06,940   adding 'pmx/_pmx.cpython-313-arm-linux-gnueabihf.so'
2026-03-23T15:48:06,943   adding 'pmx/_version.py'
2026-03-23T15:48:06,962   adding 'pmx/_xdrio.cpython-313-arm-linux-gnueabihf.so'
2026-03-23T15:48:06,970   adding 'pmx/alchemy.py'
2026-03-23T15:48:06,973   adding 'pmx/analysis.py'
2026-03-23T15:48:06,975   adding 'pmx/atom.py'
2026-03-23T15:48:06,977   adding 'pmx/atomselection.py'
2026-03-23T15:48:06,979   adding 'pmx/builder.py'
2026-03-23T15:48:06,983   adding 'pmx/chain.py'
2026-03-23T15:48:06,986   adding 'pmx/estimators.py'
2026-03-23T15:48:06,989   adding 'pmx/ffparser.py'
2026-03-23T15:48:06,999   adding 'pmx/forcefield.py'
2026-03-23T15:48:07,001   adding 'pmx/geometry.py'
2026-03-23T15:48:07,003   adding 'pmx/gmx.py'
2026-03-23T15:48:07,004   adding 'pmx/jobscript.py'
2026-03-23T15:48:07,013   adding 'pmx/library.py'
2026-03-23T15:48:07,025   adding 'pmx/ligand_alchemy.py'
2026-03-23T15:48:07,031   adding 'pmx/model.py'
2026-03-23T15:48:07,034   adding 'pmx/molecule.py'
2026-03-23T15:48:07,036   adding 'pmx/mutdb.py'
2026-03-23T15:48:07,038   adding 'pmx/ndx.py'
2026-03-23T15:48:07,040   adding 'pmx/options.py'
2026-03-23T15:48:07,041   adding 'pmx/parser.py'
2026-03-23T15:48:07,043   adding 'pmx/resselection.py'
2026-03-23T15:48:07,045   adding 'pmx/rosetta.py'
2026-03-23T15:48:07,048   adding 'pmx/rosetta_analyze.py'
2026-03-23T15:48:07,049   adding 'pmx/rotamer.py'
2026-03-23T15:48:07,051   adding 'pmx/summary.py'
2026-03-23T15:48:07,054   adding 'pmx/utils.py'
2026-03-23T15:48:07,055   adding 'pmx/xdrfile.py'
2026-03-23T15:48:07,057   adding 'pmx/xtc.py'
2026-03-23T15:48:07,084   adding 'pmx/data/aminoacids.pkl'
2026-03-23T15:48:08,886   adding 'pmx/data/bbdep.pkl'
2026-03-23T15:48:08,995   adding 'pmx/data/blosum62_new.mat'
2026-03-23T15:48:09,010   adding 'pmx/data/bp.pkl'
2026-03-23T15:48:09,029   adding 'pmx/data/bp_amber.pkl'
2026-03-23T15:48:09,050   adding 'pmx/data/bp_charmm.pkl'
2026-03-23T15:48:09,059   adding 'pmx/data/rna.pkl'
2026-03-23T15:48:09,062   adding 'pmx/data/mutff/atommass.dat'
2026-03-23T15:48:09,063   adding 'pmx/data/mutff/elements.dat'
2026-03-23T15:48:09,065   adding 'pmx/data/mutff/residuetypes.dat'
2026-03-23T15:48:09,071   adding 'pmx/data/mutff/spc216.gro'
2026-03-23T15:48:09,072   adding 'pmx/data/mutff/specbond.dat'
2026-03-23T15:48:09,073   adding 'pmx/data/mutff/vdwradii.dat'
2026-03-23T15:48:09,074   adding 'pmx/data/mutff/xlateat.dat'
2026-03-23T15:48:09,076   adding 'pmx/data/mutff/amber14sbmut.ff/Makefile.am'
2026-03-23T15:48:09,078   adding 'pmx/data/mutff/amber14sbmut.ff/Makefile.in'
2026-03-23T15:48:09,080   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.arn'
2026-03-23T15:48:09,081   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb'
2026-03-23T15:48:09,083   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb'
2026-03-23T15:48:09,084   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb'
2026-03-23T15:48:09,085   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b'
2026-03-23T15:48:09,092   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp'
2026-03-23T15:48:09,094   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd'
2026-03-23T15:48:09,096   adding 'pmx/data/mutff/amber14sbmut.ff/atomtypes.atp'
2026-03-23T15:48:09,097   adding 'pmx/data/mutff/amber14sbmut.ff/dna.arn'
2026-03-23T15:48:09,098   adding 'pmx/data/mutff/amber14sbmut.ff/dna.hdb'
2026-03-23T15:48:09,099   adding 'pmx/data/mutff/amber14sbmut.ff/dna.r2b'
2026-03-23T15:48:09,102   adding 'pmx/data/mutff/amber14sbmut.ff/dna.rtp'
2026-03-23T15:48:09,109   adding 'pmx/data/mutff/amber14sbmut.ff/ffbonded.itp'
2026-03-23T15:48:09,111   adding 'pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp'
2026-03-23T15:48:09,112   adding 'pmx/data/mutff/amber14sbmut.ff/forcefield.doc'
2026-03-23T15:48:09,114   adding 'pmx/data/mutff/amber14sbmut.ff/forcefield.itp'
2026-03-23T15:48:09,115   adding 'pmx/data/mutff/amber14sbmut.ff/gbsa.itp'
2026-03-23T15:48:09,116   adding 'pmx/data/mutff/amber14sbmut.ff/ions.itp'
2026-03-23T15:48:09,295   adding 'pmx/data/mutff/amber14sbmut.ff/mutres.mtp'
2026-03-23T15:48:09,379   adding 'pmx/data/mutff/amber14sbmut.ff/mutres.rtp'
2026-03-23T15:48:09,388   adding 'pmx/data/mutff/amber14sbmut.ff/rna.arn'
2026-03-23T15:48:09,389   adding 'pmx/data/mutff/amber14sbmut.ff/rna.hdb'
2026-03-23T15:48:09,390   adding 'pmx/data/mutff/amber14sbmut.ff/rna.r2b'
2026-03-23T15:48:09,392   adding 'pmx/data/mutff/amber14sbmut.ff/rna.rtp'
2026-03-23T15:48:09,393   adding 'pmx/data/mutff/amber14sbmut.ff/spc.itp'
2026-03-23T15:48:09,394   adding 'pmx/data/mutff/amber14sbmut.ff/spce.itp'
2026-03-23T15:48:09,395   adding 'pmx/data/mutff/amber14sbmut.ff/tip3p.itp'
2026-03-23T15:48:09,396   adding 'pmx/data/mutff/amber14sbmut.ff/tip4p.itp'
2026-03-23T15:48:09,397   adding 'pmx/data/mutff/amber14sbmut.ff/tip4pew.itp'
2026-03-23T15:48:09,399   adding 'pmx/data/mutff/amber14sbmut.ff/tip5p.itp'
2026-03-23T15:48:09,400   adding 'pmx/data/mutff/amber14sbmut.ff/urea.itp'
2026-03-23T15:48:09,401   adding 'pmx/data/mutff/amber14sbmut.ff/watermodels.dat'
2026-03-23T15:48:09,404   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn'
2026-03-23T15:48:09,406   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup'
2026-03-23T15:48:09,406   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb'
2026-03-23T15:48:09,408   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb'
2026-03-23T15:48:09,409   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb'
2026-03-23T15:48:09,410   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b'
2026-03-23T15:48:09,418   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp'
2026-03-23T15:48:09,420   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd'
2026-03-23T15:48:09,422   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp'
2026-03-23T15:48:09,425   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp'
2026-03-23T15:48:09,488   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres'
2026-03-23T15:48:09,499   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp'
2026-03-23T15:48:09,500   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn'
2026-03-23T15:48:09,501   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb'
2026-03-23T15:48:09,502   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b'
2026-03-23T15:48:09,505   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp'
2026-03-23T15:48:09,506   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp'
2026-03-23T15:48:09,511   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp'
2026-03-23T15:48:09,513   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp'
2026-03-23T15:48:09,514   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc'
2026-03-23T15:48:09,515   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp'
2026-03-23T15:48:09,516   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp'
2026-03-23T15:48:09,517   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp'
2026-03-23T15:48:09,535   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp'
2026-03-23T15:48:09,545   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp'
2026-03-23T15:48:09,548   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp'
2026-03-23T15:48:09,550   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp'
2026-03-23T15:48:09,551   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn'
2026-03-23T15:48:09,552   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb'
2026-03-23T15:48:09,553   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b'
2026-03-23T15:48:09,555   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp'
2026-03-23T15:48:09,557   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp'
2026-03-23T15:48:09,558   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp'
2026-03-23T15:48:09,559   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp'
2026-03-23T15:48:09,560   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp'
2026-03-23T15:48:09,561   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp'
2026-03-23T15:48:09,562   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp'
2026-03-23T15:48:09,563   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp'
2026-03-23T15:48:09,564   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat'
2026-03-23T15:48:09,567   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn'
2026-03-23T15:48:09,568   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb'
2026-03-23T15:48:09,569   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb'
2026-03-23T15:48:09,570   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb'
2026-03-23T15:48:09,571   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b'
2026-03-23T15:48:09,579   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp'
2026-03-23T15:48:09,581   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd'
2026-03-23T15:48:09,583   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp'
2026-03-23T15:48:09,587   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp'
2026-03-23T15:48:09,649   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres'
2026-03-23T15:48:09,660   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp'
2026-03-23T15:48:09,661   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn'
2026-03-23T15:48:09,662   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb'
2026-03-23T15:48:09,663   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b'
2026-03-23T15:48:09,666   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp'
2026-03-23T15:48:09,668   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp'
2026-03-23T15:48:09,672   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp'
2026-03-23T15:48:09,673   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp'
2026-03-23T15:48:09,675   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc'
2026-03-23T15:48:09,676   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp'
2026-03-23T15:48:09,677   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp'
2026-03-23T15:48:09,678   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp'
2026-03-23T15:48:09,697   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp'
2026-03-23T15:48:09,706   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp'
2026-03-23T15:48:09,709   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp'
2026-03-23T15:48:09,712   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp'
2026-03-23T15:48:09,713   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn'
2026-03-23T15:48:09,714   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb'
2026-03-23T15:48:09,715   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b'
2026-03-23T15:48:09,717   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp'
2026-03-23T15:48:09,718   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp'
2026-03-23T15:48:09,720   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp'
2026-03-23T15:48:09,721   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp'
2026-03-23T15:48:09,722   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp'
2026-03-23T15:48:09,723   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp'
2026-03-23T15:48:09,724   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp'
2026-03-23T15:48:09,725   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp'
2026-03-23T15:48:09,727   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat'
2026-03-23T15:48:09,729   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn'
2026-03-23T15:48:09,730   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb'
2026-03-23T15:48:09,732   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb'
2026-03-23T15:48:09,733   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb'
2026-03-23T15:48:09,734   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b'
2026-03-23T15:48:09,743   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp'
2026-03-23T15:48:09,745   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd'
2026-03-23T15:48:09,747   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp'
2026-03-23T15:48:09,748   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn'
2026-03-23T15:48:09,749   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb'
2026-03-23T15:48:09,750   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b'
2026-03-23T15:48:09,752   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp'
2026-03-23T15:48:09,756   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp'
2026-03-23T15:48:09,758   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp'
2026-03-23T15:48:09,759   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc'
2026-03-23T15:48:09,761   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp'
2026-03-23T15:48:09,762   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp'
2026-03-23T15:48:09,763   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp'
2026-03-23T15:48:09,950   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp'
2026-03-23T15:48:10,041   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp'
2026-03-23T15:48:10,051   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn'
2026-03-23T15:48:10,052   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb'
2026-03-23T15:48:10,053   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b'
2026-03-23T15:48:10,056   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp'
2026-03-23T15:48:10,057   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp'
2026-03-23T15:48:10,058   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp'
2026-03-23T15:48:10,059   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp'
2026-03-23T15:48:10,060   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp'
2026-03-23T15:48:10,062   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp'
2026-03-23T15:48:10,063   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp'
2026-03-23T15:48:10,064   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp'
2026-03-23T15:48:10,065   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat'
2026-03-23T15:48:10,067   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn'
2026-03-23T15:48:10,068   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb'
2026-03-23T15:48:10,070   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb'
2026-03-23T15:48:10,071   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb'
2026-03-23T15:48:10,072   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b'
2026-03-23T15:48:10,076   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp'
2026-03-23T15:48:10,078   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd'
2026-03-23T15:48:10,080   adding 'pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp'
2026-03-23T15:48:10,085   adding 'pmx/data/mutff/charmm22star-mut.ff/cmap.itp'
2026-03-23T15:48:10,086   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.arn'
2026-03-23T15:48:10,087   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb'
2026-03-23T15:48:10,089   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.hdb'
2026-03-23T15:48:10,090   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb'
2026-03-23T15:48:10,091   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.rtp'
2026-03-23T15:48:10,099   adding 'pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp'
2026-03-23T15:48:10,107   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp'
2026-03-23T15:48:10,111   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp'
2026-03-23T15:48:10,124   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp'
2026-03-23T15:48:10,126   adding 'pmx/data/mutff/charmm22star-mut.ff/forcefield.doc'
2026-03-23T15:48:10,128   adding 'pmx/data/mutff/charmm22star-mut.ff/forcefield.itp'
2026-03-23T15:48:10,129   adding 'pmx/data/mutff/charmm22star-mut.ff/gb.itp'
2026-03-23T15:48:10,130   adding 'pmx/data/mutff/charmm22star-mut.ff/ions.itp'
2026-03-23T15:48:10,131   adding 'pmx/data/mutff/charmm22star-mut.ff/lipids.hdb'
2026-03-23T15:48:10,135   adding 'pmx/data/mutff/charmm22star-mut.ff/lipids.rtp'
2026-03-23T15:48:10,137   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.arn'
2026-03-23T15:48:10,290   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.mtp'
2026-03-23T15:48:10,365   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.rtp'
2026-03-23T15:48:10,373   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.arn'
2026-03-23T15:48:10,375   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb'
2026-03-23T15:48:10,376   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.hdb'
2026-03-23T15:48:10,377   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb'
2026-03-23T15:48:10,378   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.r2b'
2026-03-23T15:48:10,379   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.rtp'
2026-03-23T15:48:10,380   adding 'pmx/data/mutff/charmm22star-mut.ff/spc.itp'
2026-03-23T15:48:10,381   adding 'pmx/data/mutff/charmm22star-mut.ff/spce.itp'
2026-03-23T15:48:10,383   adding 'pmx/data/mutff/charmm22star-mut.ff/tip3p.itp'
2026-03-23T15:48:10,384   adding 'pmx/data/mutff/charmm22star-mut.ff/tip4p.itp'
2026-03-23T15:48:10,385   adding 'pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp'
2026-03-23T15:48:10,386   adding 'pmx/data/mutff/charmm22star-mut.ff/tip5p.itp'
2026-03-23T15:48:10,387   adding 'pmx/data/mutff/charmm22star-mut.ff/tips3p.itp'
2026-03-23T15:48:10,388   adding 'pmx/data/mutff/charmm22star-mut.ff/watermodels.dat'
2026-03-23T15:48:10,392   adding 'pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp'
2026-03-23T15:48:10,405   adding 'pmx/data/mutff/charmm36m-mut.ff/cmap.itp'
2026-03-23T15:48:10,490   adding 'pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp'
2026-03-23T15:48:10,620   adding 'pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp'
2026-03-23T15:48:10,631   adding 'pmx/data/mutff/charmm36m-mut.ff/forcefield.doc'
2026-03-23T15:48:10,633   adding 'pmx/data/mutff/charmm36m-mut.ff/forcefield.itp'
2026-03-23T15:48:10,634   adding 'pmx/data/mutff/charmm36m-mut.ff/gb.itp'
2026-03-23T15:48:10,635   adding 'pmx/data/mutff/charmm36m-mut.ff/ions.itp'
2026-03-23T15:48:10,636   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.arn'
2026-03-23T15:48:10,637   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb'
2026-03-23T15:48:10,639   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.hdb'
2026-03-23T15:48:10,640   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb'
2026-03-23T15:48:10,641   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.r2b'
2026-03-23T15:48:10,779   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.rtp'
2026-03-23T15:48:10,788   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.vsd'
2026-03-23T15:48:10,789   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.arn'
2026-03-23T15:48:10,953   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.mtp'
2026-03-23T15:48:11,035   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.rtp'
2026-03-23T15:48:11,060   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp'
2026-03-23T15:48:11,069   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp'
2026-03-23T15:48:11,071   adding 'pmx/data/mutff/charmm36m-mut.ff/nbfix.itp'
2026-03-23T15:48:11,072   adding 'pmx/data/mutff/charmm36m-mut.ff/spc.itp'
2026-03-23T15:48:11,073   adding 'pmx/data/mutff/charmm36m-mut.ff/spce.itp'
2026-03-23T15:48:11,074   adding 'pmx/data/mutff/charmm36m-mut.ff/tip3p.itp'
2026-03-23T15:48:11,075   adding 'pmx/data/mutff/charmm36m-mut.ff/tip4p.itp'
2026-03-23T15:48:11,076   adding 'pmx/data/mutff/charmm36m-mut.ff/watermodels.dat'
2026-03-23T15:48:11,079   adding 'pmx/extensions/pmx/Energy.c'
2026-03-23T15:48:11,081   adding 'pmx/extensions/pmx/Geometry.c'
2026-03-23T15:48:11,084   adding 'pmx/extensions/pmx/Geometry.h'
2026-03-23T15:48:11,086   adding 'pmx/extensions/pmx/cpp_test.cpp'
2026-03-23T15:48:11,087   adding 'pmx/extensions/pmx/init.c'
2026-03-23T15:48:11,088   adding 'pmx/extensions/pmx/pmx.h'
2026-03-23T15:48:11,091   adding 'pmx/extensions/pmx/wrap_Geometry.c'
2026-03-23T15:48:11,093   adding 'pmx/extensions/xdr/trr2xtc.c'
2026-03-23T15:48:11,100   adding 'pmx/extensions/xdr/xdrfile.c'
2026-03-23T15:48:11,103   adding 'pmx/extensions/xdr/xdrfile.h'
2026-03-23T15:48:11,105   adding 'pmx/extensions/xdr/xdrfile_c_test.c'
2026-03-23T15:48:11,107   adding 'pmx/extensions/xdr/xdrfile_trr.c'
2026-03-23T15:48:11,109   adding 'pmx/extensions/xdr/xdrfile_trr.h'
2026-03-23T15:48:11,110   adding 'pmx/extensions/xdr/xdrfile_xtc.c'
2026-03-23T15:48:11,112   adding 'pmx/extensions/xdr/xdrfile_xtc.h'
2026-03-23T15:48:11,114   adding 'pmx/rosetta_example/README'
2026-03-23T15:48:11,115   adding 'pmx/rosetta_example/analyze.py'
2026-03-23T15:48:11,117   adding 'pmx/rosetta_example/mut.dat'
2026-03-23T15:48:11,150   adding 'pmx/rosetta_example/plot_results.ipynb'
2026-03-23T15:48:11,243   adding 'pmx/rosetta_example/prot_zn.pdb'
2026-03-23T15:48:11,247   adding 'pmx/rosetta_example/rosetta_prepare.ipynb'
2026-03-23T15:48:11,248   adding 'pmx/rosetta_example/submit_jobscripts.py'
2026-03-23T15:48:11,250   adding 'pmx/scripts/__init__.py'
2026-03-23T15:48:11,253   adding 'pmx/scripts/analyze_dhdl.py'
2026-03-23T15:48:11,256   adding 'pmx/scripts/atomMapping.py'
2026-03-23T15:48:11,258   adding 'pmx/scripts/build_cyclic_top.py'
2026-03-23T15:48:11,259   adding 'pmx/scripts/cli.py'
2026-03-23T15:48:11,261   adding 'pmx/scripts/fill_cgenff_itp.py'
2026-03-23T15:48:11,263   adding 'pmx/scripts/fix_residue_names.py'
2026-03-23T15:48:11,265   adding 'pmx/scripts/gen_abs_restraints.py'
2026-03-23T15:48:11,272   adding 'pmx/scripts/generate_hybrid_residue.py'
2026-03-23T15:48:11,274   adding 'pmx/scripts/generate_hybrid_topology.py'
2026-03-23T15:48:11,276   adding 'pmx/scripts/hydrogen_atom_renaming.py'
2026-03-23T15:48:11,277   adding 'pmx/scripts/ligandHybrid.py'
2026-03-23T15:48:11,279   adding 'pmx/scripts/make_double_box.py'
2026-03-23T15:48:11,281   adding 'pmx/scripts/md_setup.py'
2026-03-23T15:48:11,284   adding 'pmx/scripts/mutate.py'
2026-03-23T15:48:11,289   adding 'pmx/scripts/parameterize_ligands.py'
2026-03-23T15:48:11,291   adding 'pmx/scripts/prepare_crooks_runs.py'
2026-03-23T15:48:11,292   adding 'pmx/scripts/repartition_mass.py'
2026-03-23T15:48:11,294   adding 'pmx/scripts/set_gmxlib.py'
2026-03-23T15:48:11,296   adding 'pmx/scripts/setup_abfe.py'
2026-03-23T15:48:11,298   adding 'pmx/scripts/icolos_entrypoints/__init__.py'
2026-03-23T15:48:11,299   adding 'pmx/scripts/icolos_entrypoints/assemble_systems.py'
2026-03-23T15:48:11,302   adding 'pmx_biobb-5.2.2.dist-info/licenses/LICENSE'
2026-03-23T15:48:11,304   adding 'pmx_biobb-5.2.2.dist-info/METADATA'
2026-03-23T15:48:11,305   adding 'pmx_biobb-5.2.2.dist-info/WHEEL'
2026-03-23T15:48:11,306   adding 'pmx_biobb-5.2.2.dist-info/entry_points.txt'
2026-03-23T15:48:11,306   adding 'pmx_biobb-5.2.2.dist-info/top_level.txt'
2026-03-23T15:48:11,311   adding 'pmx_biobb-5.2.2.dist-info/RECORD'
2026-03-23T15:48:11,394   removing build/bdist.linux-armv7l/wheel
2026-03-23T15:48:11,665   Building wheel for pmx-biobb (setup.py): finished with status 'done'
2026-03-23T15:48:11,800   Created wheel for pmx-biobb: filename=pmx_biobb-5.2.2-cp313-cp313-linux_armv7l.whl size=5729325 sha256=78382217c2e9914a0ceea48ec558a35eaba1e42115ff5ff5676c1e93dcdfddfc
2026-03-23T15:48:11,801   Stored in directory: /tmp/pip-ephem-wheel-cache-c683ym5o/wheels/35/48/3f/1ddaf429a60cb03da0965f3229527c1456f5672bbe4cedf5cf
2026-03-23T15:48:11,822 Successfully built pmx-biobb
2026-03-23T15:48:11,967 Removed build tracker: '/tmp/pip-build-tracker-ghh_aicw'