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Author	SHA1	Message	Date
John Chodera	ffe6ebb082	Remove unused base class for small molecule template generators	2019-11-23 21:39:32 -05:00
John Chodera	86002b5278	Draft GAFFTemplateGenerator migrated from perses branch	2019-11-23 21:39:10 -05:00
John Chodera	862a3dcf10	Update test environment.	2019-10-29 22:11:21 -07:00
John Chodera	12dfa59c34	Update AMBER conversion README	2019-10-29 22:11:13 -07:00
John Chodera	715e9c4076	Overhaul README	2019-10-29 22:11:06 -07:00
John Chodera	c218ffda7f	Update Amber conversion to AmberTools 18; split out historical GAFF conversions	2019-10-26 23:43:58 -07:00
John Chodera	54bf9e20ed	Merge pull request #78 from choderalab/molssi-cookiecutter ... Update to MolSSI cookiecutter	2019-10-26 23:43:30 -07:00
John Chodera	fc038e86d5	Still fixing travis	2019-10-26 23:31:31 -07:00
John Chodera	5abeebfbbb	Update working directory for travis	2019-10-26 23:24:31 -07:00
John Chodera	6e2603a3f3	Fix travis install	2019-10-26 22:59:25 -07:00
John Chodera	b8ee58d686	Fix travis	2019-10-26 22:45:08 -07:00
John Chodera	449d974efd	Don't use 'python setup.py develop' because symlinks are removed after install	2019-10-26 21:40:52 -07:00
John Chodera	9327445e3e	Refine tests of AMBER files	2019-10-26 21:25:10 -07:00
John Chodera	a79f910ee7	Also test AMBER and CHARMM conversion	2019-10-26 21:11:33 -07:00
John Chodera	b7956dfed7	Remove erroneous __init__.py from tests/ folder	2019-10-26 20:23:07 -07:00
John Chodera	cb3efa0b9f	Upadate paths	2019-10-26 20:21:50 -07:00
John Chodera	be575a6250	Fix issues with tests	2019-10-26 19:43:47 -07:00
John Chodera	73b0ffea3e	Relax ambertools dependency to allow both linux and osx for now	2019-10-26 19:01:11 -07:00
John Chodera	8d5bdee59d	Update to MolSSI cookiecutter	2019-10-26 18:55:15 -07:00
John Chodera	41b564d932	Update license	2019-10-26 17:27:54 -07:00
John Chodera	667048876d	Merge pull request #72 from choderalab/bugfixes ... Bugfixes and updates	2019-10-26 17:27:32 -07:00
John Chodera	9a0515e560	Add Python 3.7 support	2019-01-02 13:22:50 -08:00
John Chodera	ea55a661d1	Remove outdated manually-added parm15ipq_10.3.dat	2018-12-27 22:16:22 -08:00
John Chodera	4a12eb9f59	Update README	2018-12-27 22:08:55 -08:00
John Chodera	d2070b2cbf	Merge pull request #68 from choderalab/phosaa10 ... Add missing phosaa10.xml file 0.4.0	2018-09-11 14:44:42 -04:00
jchodera	bcab50b3be	Add missing phosaa10.xml	2018-09-11 14:44:06 -04:00
John Chodera	4c5b261acd	Merge pull request #67 from choderalab/phosaa10 ... [WIP] Add conversion of phosaa10	2018-09-11 14:42:45 -04:00
jchodera	72b8d36163	Complete conversion and testing with phosaa10	2018-09-10 18:15:15 -04:00
jchodera	87dbeee226	Add conversion of phosaa10	2018-09-10 15:53:49 -04:00
John Chodera	d33c6bb4f7	Merge pull request #66 from choderalab/ambertools18 ... Updating to AmberTools 18	2018-09-07 21:54:18 -04:00
John Chodera	3bafc291ed	Update paths for travis	2018-08-24 17:58:43 -07:00
John Chodera	59a1ad8af0	Update ambertools git branch	2018-08-24 17:48:44 -07:00
John Chodera	c4ae02e543	Update AMBER forcefield conversion to complete AmberTools18 conversion	2018-08-22 09:28:15 -07:00
John Chodera	b2f7dc228d	Update converted files	2018-08-21 13:57:32 -07:00
John Chodera	2adb1a670d	In process of updating to AmberTools 18 [incomplete]	2018-08-19 13:47:13 -07:00
John Chodera	11247d2ede	Merge pull request #64 from choderalab/unique-patches ... Update CHARMM ffxml by culling duplicate patches	2018-08-18 14:19:58 -04:00
John Chodera	b6d2e91680	Add DISU patch and add tests for CHARMM	2018-08-18 13:49:27 -04:00
jchodera	217c12a714	Regenerate CHARMM ffxml parameters using https://github.com/ParmEd/ParmEd/pull/1001	2018-08-11 19:39:12 -04:00
John Chodera	644df5a7e7	Update CHARMM ffxml by culling duplicate patches	2018-04-23 22:32:06 -04:00
John Chodera	57892fd644	Merge pull request #63 from choderalab/add-charmm-disulfide ... Manually add DISU patch and test protein with disulfide bonds	2018-04-23 21:49:03 -04:00
John Chodera	50d60d10c2	Fix bug in DISU patch definition	2018-04-16 23:51:17 -04:00
John Chodera	e767baa5df	Manually add DISU patch and tst protein with disulfide bonds	2018-04-15 19:42:52 -07:00
John Chodera	5593bfcd67	Merge pull request #62 from choderalab/fix-connections ... Update AMBER forcefields to fix CYX bug	2018-03-20 21:29:44 -04:00
John Chodera	2bec6e063d	Update AMBER ffxml conversion incorporating external connections besides tails, using latest AmberTools 17.6	2018-03-02 22:25:05 -05:00
John Chodera	e55dd6847b	Update provenance to AmberTools 17.6	2018-03-02 21:19:36 -05:00
John Chodera	104f903eb3	Merge pull request #61 from choderalab/charmm-tests ... [WIP] Adding first draft of direct comparison to CHARMM	2018-03-02 20:55:16 -05:00
John Chodera	49082f122b	Minor tweaks to tests	2018-03-02 20:54:37 -05:00
John Chodera	01048ba39d	Compare total potential energies in test_charmm.py	2018-02-19 15:29:52 -05:00
John Chodera	eecdb0a363	Print energy decomposition	2018-02-19 14:28:05 -05:00
John Chodera	69aaf5960c	Streamline energy computation	2018-02-19 14:22:51 -05:00