choderalab/openmoltools

Issues

• cannot import name 'gafftools' from 'openmoltools'

  #310 opened a year ago by kapilaGIT
  0

• Protein-ligand OpenMM example - generating chemical .xml files

  #309 opened 3 years ago by gcorso
  0

• <Atom> and <Bond> tags are not written with processAmberForceField.py when this information is available in a .lib file

  #307 opened 4 years ago by rosemary-mantell-cresset
  1

• Remove forcefield generators

  #305 opened 4 years ago by jchodera
  0

• Updates for new OpenMM namespace

  #303 opened 4 years ago by jaimergp
  7

• Update conda recipe to use ambertools

  #278 opened 4 years ago by jchodera
  3

• ParmEd Error with AmberTools ==20.0

  #301 opened 5 years ago by SimonBoothroyd
  2

• Incorrect checking of ParmEd version

  #273 opened 5 years ago by jchodera
  0

• typo in docstring of openeye.py

  #300 opened 5 years ago by vtlim
  0

• run_tleap raises exception running on Ambertools 19

  #299 opened 5 years ago by badisa
  0

• packmol bond order error

  #287 opened 6 years ago by guoweiqi
  1

• `generateOEMolFromTopologyResidue` failing in perses tests

  #295 opened 5 years ago by hannahbrucemacdonald
  4

• Why is generateOEMolFromTopologyResidue line 137 commented out?

  #279 opened 5 years ago by zhang-ivy
  0

• Issues recognizing GAFF2 atom type

  #292 opened 5 years ago by eventfulsean
  0

• Clean up openmoltools/chemicals

  #286 opened 6 years ago by jchodera
  0

• Change forcefield_generators.generateOEMolFromTopologyResidue to use molecule_to_mol2

  #284 opened 6 years ago by jchodera
  2

• Update travis tests and repository structure to use MolSSI cookiecutter

  #283 opened 6 years ago by jchodera
  0

• generateOEMolFromTopologyResidue sometimes fails on `osx` due to non-UTF-8 character

  #271 opened 6 years ago by jchodera
  5

• smiles_to_antechamber does not use a protonation model

  #280 opened 6 years ago by davidlmobley
  0

• Unable to get the correct tleap comand with build_mixture_prmtop

  #277 opened 7 years ago by jy634
  0

• Scripts should not go in bin

  #232 opened 7 years ago by wesbarnett
  4

• openeye.get_charges() emits warning

  #276 opened 7 years ago by jchodera
  2

• Better way to select between legacy OEAssignPartialCharges and OEAssignCharges

  #270 opened 7 years ago by jchodera
  0

• Do a new release

  #257 opened 7 years ago by davidlmobley
  2

• Migration of forcefield_generators.py to openmm-forcefields

  #256 opened 8 years ago by jchodera
  0

• Packmol code fails to introduce CONECT entries whenever one of the molecules involved is water

  #253 opened 8 years ago by davidlmobley
  21

• Migrate to new OpenEye charging engine

  #252 opened 8 years ago by davidlmobley
  1

• Re-license to MIT

  #246 opened 8 years ago by davidlmobley
  7

• Potential python 3.x issue in calling ambertools

  #244 opened 8 years ago by jchodera
  0

• AmberParser bug with Ambertools16 gaff.dat

  #235 opened 8 years ago by bas-rustenburg
  15

• Importing amber module leads to ValueError

  #236 opened 8 years ago by bas-rustenburg
  1

• Direct manipulation of mol2 files

  #231 opened 9 years ago by andrrizzi
  5

• Packmol error

  #223 opened 9 years ago by jchodera
  4

• Add more informative error messages when `get_charges` fails

  #230 opened 9 years ago by jchodera
  0

• Errors with `get charges` in `generateResidueTemplete`

  #229 opened 9 years ago by gregoryross
  6

• Add more informative output to the force comparison in system_checker

  #227 opened 9 years ago by davidlmobley
  4

• Segmentation fault with `gaffTemplateGenerator`

  #226 opened 9 years ago by gregoryross
  5

• Fixing packmol tests to work without RDKit

  #221 opened 9 years ago by davidlmobley
  2

• Debug issues with generateForceFieldFromMolecules

  #224 opened 9 years ago by jchodera
  0

• OpenEye beta will fail on travis due to ubuntu compatibility

  #219 opened 9 years ago by davidlmobley
  4

• utils.randomize_residue_names changes bond types

  #216 opened 9 years ago by davidlmobley
  1

• Adding protons

  #218 opened 9 years ago by jchodera
  0

• openmoltools.openeye.molecule_to_mol2 changes atom names

  #215 opened 9 years ago by jchodera
  8

• Allow charge generation to fail gracefully

  #208 opened 9 years ago by pgrinaway
  2

• Lots of OpenEye warnings

  #201 opened 9 years ago by jchodera
  24

• py3.5 error

  #202 opened 9 years ago by jchodera
  3

• Keep old indices somewhere after generateOEMolFromTopologyResidue

  #203 opened 9 years ago by pgrinaway
  3

• Remove logging configuration in openmoltools modules

  #194 opened 9 years ago by andrrizzi
  3

• Have openmoltools-dev build for multiple platforms

  #192 opened 9 years ago by jchodera
  0

• generateTopologyFromOEMol adds bonds from one atom to itself.

  #191 opened 9 years ago by pgrinaway
  2