openmmforcefields

RustOpenMM/openmmforcefields

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67f51045e1 Rename CHARMM metapackage John Chodera 2017-11-19 12:47:03 -05:00
489b19e178 Add CHARMM ffxml metapackage John Chodera 2017-11-19 12:13:15 -05:00
505614082f Add --verbose flags to charmm conversion John Chodera 2017-11-19 12:12:27 -05:00
cf33986116 Update CHARMM36 no-waters YAML John Chodera 2017-11-19 12:12:03 -05:00
e8d50be977 Remove old (unused) CHARMM yaml files and ffxml files John Chodera 2017-11-19 12:04:42 -05:00
46e4e7ad9a Split out waters from CHARMM36 forcefield conversion. John Chodera 2017-11-19 12:03:29 -05:00
c2f60f317f Merge pull request #43 from choderalab/amber John Chodera 2017-10-29 12:48:30 -07:00
a5411b52f7 fix master Rafal P. Wiewiora 2017-10-28 14:45:20 -04:00
14e4ce8269 add tip3pfb and tip4pfb; add master Rafal P. Wiewiora 2017-10-28 14:43:38 -04:00
e433dcb566 add tip3p-fb and tip4p-fb Rafal P. Wiewiora 2017-10-28 14:31:33 -04:00
e98512dc33 Split out default waters from CHARMM36 conversion. This will need some parmed fixes for line continuation characters. John Chodera 2017-10-21 23:31:40 -04:00
9edcd230b0 CHARMM conversion script can now generate multiple distinct forcefields; convert waters separately. John Chodera 2017-10-21 21:29:36 -04:00
74381fe2df Merge pull request #41 from choderalab/amber John Chodera 2017-10-21 10:00:43 -04:00
84d620f58d Update travis John Chodera 2017-10-21 00:13:18 -04:00
dec5ba4da2 Update conversion and add merged lipids. John Chodera 2017-10-20 23:58:18 -04:00
c290f8f7f6 Remove special characters from master.yaml John Chodera 2017-10-20 22:55:47 -04:00
94d20dc13e Provide more useful LEaP failure messages with LeapException John Chodera 2017-10-20 18:38:53 -04:00
66baab6a24 Update README John Chodera 2017-10-20 18:38:46 -04:00
23478dfba7 Change lipids test to *just* use lipids John Chodera 2017-10-20 18:11:20 -04:00
ecfcd23416 Add DOPC test system for Amber lipids John Chodera 2017-10-20 17:38:03 -04:00
a020f33909 Add draft automated energy test for lipids system using DOPC ligands from http://ambermd.org/tutorials/advanced/tutorial16/#Lipid_Bilayer_Structures John Chodera 2017-10-20 17:37:08 -04:00
2d952e175b Add merge_lipids.py to travis John Chodera 2017-10-20 17:34:01 -04:00
c7b85241eb Add generation of ffxml/lipid17_unmerged.xml to master.yaml John Chodera 2017-10-20 17:33:26 -04:00
51f52371e0 Add Amber17 manual for reference John Chodera 2017-10-20 16:51:37 -04:00
dc8b2d6bb8 Add charmmlipid2amber.csv from AmberTools17 John Chodera 2017-10-20 16:48:41 -04:00
aeab39a7cf Add documentation on lipid merging script to README John Chodera 2017-10-20 15:02:32 -04:00
4f63cc5467 Merge pull request #40 from peastman/merge John Chodera 2017-10-20 14:51:32 -04:00
ee735210a8 Created script for merging lipids peastman 2017-10-09 12:16:51 -07:00
d5af3e5aba Merge pull request #39 from choderalab/fix-travis John Chodera 2017-10-07 09:08:04 -04:00
6319afe01a Remove outdated lipids-only conversion. John Chodera 2017-10-07 09:06:08 -04:00
1621875aa2 Shave some more time off John Chodera 2017-10-06 22:42:47 -04:00
2e0c62c450 Exclude D-amino acids from CHARMM conversion John Chodera 2017-10-06 22:10:42 -04:00
8f994dcf67 Update AMBER conversion with new lxml-based XML writing John Chodera 2017-10-06 21:43:30 -04:00
c883354a5c Force update after conda-forge channel added jchodera 2017-10-05 15:51:02 -04:00
bb694fe9a4 Add NetworkX jchodera 2017-10-05 15:29:41 -04:00
68923a9264 Merge pull request #37 from choderalab/amber John Chodera 2017-10-05 13:59:40 -04:00
aa28a7e420 Update all AMBER forcefield files for AmberTools 17 jchodera 2017-10-05 13:57:40 -04:00
7af296b0a3 Unicode characters in author names were causing trouble with parmed jchodera 2017-10-05 13:19:07 -04:00
29ae1a173a add all references, add one RNA ff Rafal P. Wiewiora 2017-10-04 18:53:12 -04:00
f2c71301f6 change residue overload_level to override_level - fix ions Rafal P. Wiewiora 2017-10-04 12:11:40 -04:00
563700309d Use --verbose flag for convert_amber.py jchodera 2017-09-29 20:48:04 -04:00
2597a98db8 Merge pull request #35 from choderalab/amber John Chodera 2017-09-29 20:46:21 -04:00
e869e1e621 Support python 2.7 in write_file jchodera 2017-09-29 20:32:44 -04:00
9a4d79149d Fix file opening for amber file writing jchodera 2017-09-29 20:24:16 -04:00
80dbe50c6b Install parmed from git jchodera 2017-09-29 20:11:12 -04:00
05e9d95947 Add lxml dependency jchodera 2017-09-29 20:00:20 -04:00
47a260064a Install pyyaml jchodera 2017-09-29 19:38:42 -04:00
22a26297af More python3 conversions jchodera 2017-09-29 19:34:25 -04:00
55fd2eef6f Write OpenMM ffxml files with 'amber' style impropers jchodera 2017-09-29 19:22:54 -04:00
2b9349aac8 Make convert_amber.py python3 compatible jchodera 2017-09-29 18:48:16 -04:00
d4da0382d0 Use ambertools 17 jchodera 2017-09-29 18:14:57 -04:00
62ea34f31e Install ambermini instead of ambertools since ambertools appears to be broken. jchodera 2017-09-29 18:04:50 -04:00
059ab28cdf Add ambertools dependency; remove build-time dependencies jchodera 2017-09-29 17:26:10 -04:00
642c5d3f29 Update travis and conda-recipe jchodera 2017-09-29 17:24:47 -04:00
e1f2f99177 UpdaMerge branch 'master' of github.com:choderalab/openmm-forcefields jchodera 2017-09-06 14:57:33 -04:00
1dea5cfb8e Verify written ffxml file can be read by app.ForceField John Chodera 2017-09-06 08:53:07 -04:00
7553d4995b Debug code jchodera 2017-09-05 17:57:28 -04:00
fa96a03d7d Merge pull request #26 from choderalab/travis 0.1.0 John Chodera 2017-06-30 11:24:52 -04:00
9c6ff2466a Install yaml too John Chodera 2017-06-24 00:07:41 -04:00
02c6351359 Add parmed John Chodera 2017-06-23 23:58:39 -04:00
7b0d424f2c Update meta.yaml John Chodera 2017-06-23 23:48:16 -04:00
b81eba9f50 Fix typo John Chodera 2017-06-23 23:41:15 -04:00
b19f814d37 Add __init__.py John Chodera 2017-06-23 23:30:11 -04:00
87b2fae7c9 More nosetest improvements. John Chodera 2017-06-23 23:28:34 -04:00
db415b6768 Try to get tests to run on travis John Chodera 2017-06-23 23:17:36 -04:00
a50fba557f Update setup to install tests subpackage John Chodera 2017-06-23 22:48:34 -04:00
62b7f3db05 Rename AMBER conversion script John Chodera 2017-06-23 22:31:57 -04:00
85fbd0425f Revise travis John Chodera 2017-06-23 22:30:13 -04:00
eb66ee4dcb AMBER installation works; added tests John Chodera 2017-06-23 22:27:50 -04:00
f4e0a908d1 Fix typo John Chodera 2017-06-23 15:03:52 -04:00
2ee2b22ed6 Initial draft of setup.py and autodiscovery John Chodera 2017-06-23 14:57:03 -04:00
2b70e68b42 Merge remote-tracking branch 'origin/master' into travis John Chodera 2017-06-04 13:43:26 -04:00
9356e9a178 Fix error in build.sh John Chodera 2017-04-23 23:26:33 -04:00
a41fc28bee Fix build script John Chodera 2017-04-23 21:31:37 -04:00
339c0b2e8e Open files for reading in binary format when computing md5 hash (for py3 compatibility) John Chodera 2017-04-23 21:27:34 -04:00
fb72a1007c Merge pull request #27 from choderalab/amber Rafal Wiewiora 2017-04-20 13:14:07 -07:00
de2b46da1c add dependencies and testing instructions to README Rafal P. Wiewiora 2017-04-20 16:13:14 -04:00
5e26b3996b initial amber commit - copy from choderalab/openmm Rafal P. Wiewiora 2017-04-18 12:15:50 -04:00
2bcb87ed9f Update recipe jchodera 2017-04-17 14:07:14 -04:00
6241305286 Update CHARMM README jchodera 2017-04-17 13:55:02 -04:00
f67e873dc8 Add travis badge to README jchodera 2017-04-17 13:49:36 -04:00
2a590b23e4 Add travis boilerplate jchodera 2017-04-17 13:48:10 -04:00
98e57c3725 Merge pull request #1 from ChayaSt/charmm36 Chaya Stern 2017-03-23 16:16:11 -04:00
113d824fb4 converted some lipids ChayaSt 2017-03-02 12:13:38 -05:00
f94144ea1b migrated from openmm ChayaSt 2017-03-01 17:50:23 -05:00
f6b5513b85 Initial commit John Chodera 2016-10-05 16:26:35 -07:00

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