choderalab openmoltools issues

choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules

MIT License

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issues

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cannot import name 'gafftools' from 'openmoltools'

#310 kapilaGIT opened 11 months ago
0
Protein-ligand OpenMM example - generating chemical .xml files

#309 gcorso opened 2 years ago
0
Update README.md

#308 richardjgowers closed 3 years ago
0
<Atom> and <Bond> tags are not written with processAmberForceField.py when this information is available in a .lib file

#307 rosemary-mantell-cresset closed 3 years ago
1
Update CI.yaml

#306 mikemhenry closed 3 years ago
0
Remove forcefield generators

#305 jchodera opened 3 years ago
0
Update for OpenMM namespace changes

#304 mikemhenry closed 3 years ago
10
Updates for new OpenMM namespace

#303 jaimergp closed 3 years ago
7
Remove unneeded deps in setup.py

#302 jaimergp closed 3 years ago
1
ParmEd Error with AmberTools ==20.0

#301 SimonBoothroyd closed 4 years ago
2
typo in docstring of openeye.py

#300 vtlim opened 4 years ago
0
run_tleap raises exception running on Ambertools 19

#299 badisa opened 4 years ago
0
Remove travis badge from README

#298 jchodera closed 4 years ago
0
Fix warnings with bondtype

#297 jchodera closed 4 years ago
2
reverting back to using bondtype instead of antechamber

#296 hannahbrucemacdonald closed 4 years ago
0
`generateOEMolFromTopologyResidue` failing in perses tests

#295 hannahbrucemacdonald closed 4 years ago
4
Fixes `packmol` module compatibility with recent OpenMM and MDTraj versions

#294 davidlmobley closed 4 years ago
2
[WIP] Use conda-forge ambertools for tests

#293 jchodera closed 4 years ago
0
Issues recognizing GAFF2 atom type

#292 eventfulsean opened 5 years ago
0
Update openeye.py

#291 hannahbrucemacdonald closed 5 years ago
0
[WIP] updating to openeye charging methods

#290 hannahbrucemacdonald closed 5 years ago
2
fix for not including tleap summary message as an error

#289 ajsilveira closed 4 years ago
1
fixing forcefield_generators to be compatible with openmm 7.4

#288 hannahbrucemacdonald closed 5 years ago
1
packmol bond order error

#287 guoweiqi opened 5 years ago
1
Clean up openmoltools/chemicals

#286 jchodera opened 5 years ago
0
Add new OEGAFFTemplateGenerator

#285 jchodera closed 4 years ago
3
Change forcefield_generators.generateOEMolFromTopologyResidue to use molecule_to_mol2

#284 jchodera opened 5 years ago
2
Update travis tests and repository structure to use MolSSI cookiecutter

#283 jchodera opened 5 years ago
0
Update bond order perception and pre-generate residue templates

#282 zhang-ivy opened 6 years ago
0
Modify `smiles_to_antechamber` to allow optional use of protonation model

#281 davidlmobley closed 6 years ago
3
smiles_to_antechamber does not use a protonation model

#280 davidlmobley closed 6 years ago
0
Why is generateOEMolFromTopologyResidue line 137 commented out?

#279 zhang-ivy closed 4 years ago
0
Update conda recipe to use ambertools

#278 jchodera closed 3 years ago
3
Unable to get the correct tleap comand with build_mixture_prmtop

#277 jy634 opened 6 years ago
0
openeye.get_charges() emits warning

#276 jchodera opened 6 years ago
2
Fix forcefield generators to work with latest ParmEd

#275 jchodera opened 6 years ago
1
Don't raise a ParmEd version exception if parmed.version reports (0,0,0) due to dirty install

#274 jchodera closed 4 years ago
3
Incorrect checking of ParmEd version

#273 jchodera closed 4 years ago
0
Fix #271

#272 jchodera closed 5 years ago
7
generateOEMolFromTopologyResidue sometimes fails on `osx` due to non-UTF-8 character

#271 jchodera closed 5 years ago
5
Better way to select between legacy OEAssignPartialCharges and OEAssignCharges

#270 jchodera opened 6 years ago
0
Write out multiple conformers

#269 ChayaSt closed 6 years ago
6
Bump to 0.9.0

#268 Lnaden closed 6 years ago
0
Cut official 0.8.3 release - Final Py27

#267 Lnaden closed 6 years ago
0
Remove Libgfortran dependency pin

#266 Lnaden closed 6 years ago
13
Deactivate release and bump version

#265 Lnaden closed 6 years ago
0
Update encrypted OpenEye license

#264 jchodera closed 6 years ago
1
Make OEIUPAC optional for normalize_molecule, cut release

#263 Lnaden closed 6 years ago
3
Update for ongoing development of 0.8.2

#262 andrrizzi closed 7 years ago
0
Apply packmol docs suggestions for box size with PBC

#261 andrrizzi closed 7 years ago
12