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• b6b1aa3903 Merge pull request #82 from choderalab/update-readme John Chodera 2020-01-07 17:45:18 -05:00
• f0a517af0e Add 0.6.1 release notes John Chodera 2020-01-07 17:44:16 -05:00
• 5104bb3ca6 Fix docs and minor issues with GAFF version retrieval John Chodera 2020-01-07 17:41:57 -05:00
• 671a6218a5 Add hacky install method John Chodera 2020-01-07 17:19:37 -05:00
• 560829d0e2 Merge pull request #81 from choderalab/update-amber 0.6.0 John Chodera 2020-01-05 21:37:01 -08:00
• 2d714b6977 Update README John Chodera 2020-01-06 00:36:30 -05:00
• 5d9f8f3077 Merge pull request #79 from choderalab/update-amber John Chodera 2020-01-05 19:57:25 -08:00
• c03da47850 Fix travis John Chodera 2020-01-05 19:30:47 -08:00
• f18af600df Use openeye toolkits to speed up tests John Chodera 2020-01-05 18:08:17 -08:00
• 7444eaccc4 Fix wget typo John Chodera 2020-01-05 16:53:10 -08:00
• 6e610a4de5 Use https://github.com/openmm/openmm/pull/2511 fix on travis John Chodera 2020-01-05 16:38:17 -08:00
• 9b55c27287 Fix tests John Chodera 2020-01-05 11:49:49 -08:00
• cc200726b6 Update documentation John Chodera 2020-01-05 11:49:42 -08:00
• 83dff0b7e6 Add add_molecules to SystemGenerator John Chodera 2020-01-04 18:06:15 -08:00
• b11db2098a Update tests for SystemGenerator John Chodera 2020-01-04 16:57:06 -08:00
• 86967c642c Update requirements to openmm >=7.5.0 for smirnoff updates John Chodera 2020-01-04 16:06:30 -08:00
• 26907ef23b Fix test John Chodera 2020-01-04 15:25:13 -08:00
• 0533d21e50 Fix tests John Chodera 2020-01-04 15:19:11 -08:00
• 51a1006efa Template generator tests should all pass now! John Chodera 2020-01-04 12:23:42 -08:00
• f3cb63443f Fix typo John Chodera 2020-01-04 12:18:04 -08:00
• f4a6282e13 Test explicit solvent systems as well. John Chodera 2020-01-04 12:17:40 -08:00
• 08aebe7224 Restrict protein-ligand JACS set tests to only those complexes with working input files John Chodera 2020-01-04 12:07:51 -08:00
• 84acb15dc8 Use PDBFile -> ParmEd Structure workaround for loading protein files. John Chodera 2020-01-03 15:52:34 -08:00
• 47fbf2dfb5 Try deleting and re-adding protons on terminal protein residues John Chodera 2020-01-03 13:14:35 -08:00
• 06dea05c59 Fix issues with torsion periodicity; more work on SystemGenerators John Chodera 2020-01-02 23:35:17 -08:00
• 5f83edb3c3 Add test for forces John Chodera 2019-12-30 13:53:46 -08:00
• 44e624bdb2 Make sure to remove constraints from SMIRNOFF handler when parameterizing small molecule force fields. John Chodera 2019-12-29 09:12:05 -08:00
• 173b366f4a Fix remaining test failures John Chodera 2019-12-28 09:54:26 -08:00
• 81c77d7162 Update README John Chodera 2019-12-27 21:05:52 -08:00
• 50e7b1b70b Fix test errors after API improvements. John Chodera 2019-12-27 14:19:45 -08:00
• b89898389d Harmonize template generator APIs John Chodera 2019-12-27 12:09:18 -08:00
• 0452e6be4c Add missing Tyk2 ligands file from https://github.com/brycestx/perses_jacs_systems/pull/3 John Chodera 2019-12-27 10:54:11 -08:00
• 295c73b877 Update logic for selecting number of molecules to use in travis tests John Chodera 2019-12-27 09:45:07 -08:00
• ad7f1c1240 Try to speed up tests for travis John Chodera 2019-12-26 10:09:31 -08:00
• 6c422f381f Reduce number of tests for travis John Chodera 2019-12-25 23:14:02 -08:00
• 602b572333 Reduce number of molecules tested for travis John Chodera 2019-12-25 23:10:39 -08:00
• aa1b6687cc Reduce the number of molecules per system being tested on travis John Chodera 2019-12-24 21:36:58 -08:00
• 1bb06233fd All tests pass locally (except for incomplete SystemGenerator tests); update travis John Chodera 2019-12-24 17:15:54 -08:00
• 2fe8c45c1b Fix GAFF test issue John Chodera 2019-12-24 16:57:44 -08:00
• 4cf17610b0 SMIRNOFFTemplateGenerator tests now pass John Chodera 2019-12-24 16:43:10 -08:00
• ebff404863 Debug various aspects of new residue template generators John Chodera 2019-12-22 15:47:51 -05:00
• 764ad2f79d More debugging John Chodera 2019-12-22 13:36:15 -05:00
• bba6335ac8 Filter out MiniDrugBank molecules with unspecified stereochemistry John Chodera 2019-12-22 13:35:59 -05:00
• 474400ead9 Initial draft of SMIRNOFFTemplateGenerator John Chodera 2019-12-22 12:15:53 -05:00
• 3024f97d1e Further refine README and SystemGenerator concept John Chodera 2019-12-21 20:38:30 -05:00
• d1d32b7851 Fix typos John Chodera 2019-12-21 20:26:46 -05:00
• d5602bc83c Update README with refined concept for SystemGenerator John Chodera 2019-12-21 20:25:16 -05:00
• b7ab3fa893 Cleanup John Chodera 2019-12-21 19:28:35 -05:00
• 5876038cec Update README John Chodera 2019-12-21 18:40:00 -05:00
• 8466b5ede0 Add test for Modeller.add_solvent John Chodera 2019-11-30 21:39:53 -05:00
• 5bb7c18927 Better suppression of debug info during tests John Chodera 2019-11-30 18:58:13 -05:00
• bd94f8cf79 Add JACS test systems John Chodera 2019-11-30 18:49:26 -05:00
• 6245bf383c Add wwarning that CHARMM force fields have not yet been fully validated John Chodera 2019-11-30 11:47:30 -05:00
• 9927eab2d8 Add missing waterbox test files John Chodera 2019-11-30 11:46:24 -05:00
• ff9719a89b Merge branch 'update-amber' of github.com:choderalab/openmm-forcefields into update-amber John Chodera 2019-11-30 11:21:42 -05:00
• 3f880ac840 Allow osx tests by backing off on required AmberTools version John Chodera 2019-11-30 10:33:20 -05:00
• b7ae2e26f1 Add minidrugbank John Chodera 2019-11-29 22:15:18 -05:00
• c651f63630 Update AMBER conversion script for new GAFF paths John Chodera 2019-11-29 22:12:46 -05:00
• 0bf4ba3e5f Fix paths for GAFF conversion John Chodera 2019-11-29 22:09:43 -05:00
• e884280d5d GAFFTemplateGenerator tests pass locally! John Chodera 2019-11-29 21:36:34 -05:00
• 2ab75f849e Migrate GAFF to amber/gaff/{ffxml,dat} John Chodera 2019-11-29 18:02:43 -05:00
• 0d7d4b579e Add merge_lipids.py and missing merged lipid17 ffxml John Chodera 2019-11-29 18:02:21 -05:00
• c85f458105 Update AMBER force fields with AmberTools 19.9 John Chodera 2019-11-29 16:32:10 -05:00
• 6f9ad42ce3 Fix typo in leaprc.gaff John Chodera 2019-11-29 16:29:28 -05:00
• 89b1328b5a Update generators and setup.py John Chodera 2019-11-29 11:58:40 -05:00
• a2d12b066f Modify conversion script energy test log to be able to specify filename John Chodera 2019-11-29 11:58:08 -05:00
• 41d6ee8185 Add GAFF 1.7 and regenerate GAFF force fields with AmberTools 19 John Chodera 2019-11-29 11:47:42 -05:00
• 046e46e84c Add __init__.py for generators John Chodera 2019-11-23 21:40:13 -05:00
• 3af2711291 Add draft tests for template generators John Chodera 2019-11-23 21:39:59 -05:00
• ffe6ebb082 Remove unused base class for small molecule template generators John Chodera 2019-11-23 21:39:32 -05:00
• 86002b5278 Draft GAFFTemplateGenerator migrated from perses branch John Chodera 2019-11-23 21:39:10 -05:00
• 862a3dcf10 Update test environment. John Chodera 2019-10-29 22:11:21 -07:00
• 12dfa59c34 Update AMBER conversion README John Chodera 2019-10-29 22:11:13 -07:00
• 715e9c4076 Overhaul README John Chodera 2019-10-29 22:11:06 -07:00
• c218ffda7f Update Amber conversion to AmberTools 18; split out historical GAFF conversions John Chodera 2019-10-26 23:43:58 -07:00
• 54bf9e20ed Merge pull request #78 from choderalab/molssi-cookiecutter John Chodera 2019-10-26 23:43:30 -07:00
• fc038e86d5 Still fixing travis John Chodera 2019-10-26 23:31:31 -07:00
• 5abeebfbbb Update working directory for travis John Chodera 2019-10-26 23:24:31 -07:00
• 6e2603a3f3 Fix travis install John Chodera 2019-10-26 22:59:25 -07:00
• b8ee58d686 Fix travis John Chodera 2019-10-26 22:45:08 -07:00
• 449d974efd Don't use 'python setup.py develop' because symlinks are removed after install John Chodera 2019-10-26 21:40:52 -07:00
• 9327445e3e Refine tests of AMBER files John Chodera 2019-10-26 21:25:10 -07:00
• a79f910ee7 Also test AMBER and CHARMM conversion John Chodera 2019-10-26 21:11:33 -07:00
• b7956dfed7 Remove erroneous __init__.py from tests/ folder John Chodera 2019-10-26 20:23:07 -07:00
• cb3efa0b9f Upadate paths John Chodera 2019-10-26 20:21:50 -07:00
• be575a6250 Fix issues with tests John Chodera 2019-10-26 19:43:47 -07:00
• 73b0ffea3e Relax ambertools dependency to allow both linux and osx for now John Chodera 2019-10-26 19:01:11 -07:00
• 8d5bdee59d Update to MolSSI cookiecutter John Chodera 2019-10-26 18:55:15 -07:00
• 41b564d932 Update license John Chodera 2019-10-26 17:27:54 -07:00
• 667048876d Merge pull request #72 from choderalab/bugfixes John Chodera 2019-10-26 17:27:32 -07:00
• 9a0515e560 Add Python 3.7 support John Chodera 2019-01-02 13:22:50 -08:00
• ea55a661d1 Remove outdated manually-added parm15ipq_10.3.dat John Chodera 2018-12-27 22:16:22 -08:00
• 4a12eb9f59 Update README John Chodera 2018-12-27 22:08:55 -08:00
• d2070b2cbf Merge pull request #68 from choderalab/phosaa10 0.4.0 John Chodera 2018-09-11 14:44:42 -04:00
• bcab50b3be Add missing phosaa10.xml jchodera 2018-09-11 14:44:06 -04:00
• 4c5b261acd Merge pull request #67 from choderalab/phosaa10 John Chodera 2018-09-11 14:42:45 -04:00
• 72b8d36163 Complete conversion and testing with phosaa10 jchodera 2018-09-10 18:15:15 -04:00
• 87dbeee226 Add conversion of phosaa10 jchodera 2018-09-10 15:53:49 -04:00
• d33c6bb4f7 Merge pull request #66 from choderalab/ambertools18 John Chodera 2018-09-07 21:54:18 -04:00
• 3bafc291ed Update paths for travis John Chodera 2018-08-24 17:58:43 -07:00