OpenBioSim/biosimspace

Issues

• [BUG] MIssing Windows Python 3.10 package for 2024.3.0 release

  #358 opened a month ago by lohedges
  0

• [BUG] PrepareFep creates coordinate mismatch between protein and ligand

  #354 opened a month ago by mark-mackey-cresset
  4

• What about ff99-disp

  #346 opened 2 months ago by bcossins
  6

• [BUG] Update hydration free energy tutorial with new 2D mapping view

  #350 opened 2 months ago by lohedges
  0

• [BUG] Use direct to/from RDKit conversion when parameterising with OpenFF

  #348 opened 2 months ago by lohedges
  0

• [BUG] Merge code no longer setting a unique connectivty property when connectivity changes

  #344 opened 2 months ago by lohedges
  0

• Negatively charged nitrogen parameterisation

  #347 opened 2 months ago by noahharrison64
  2

• Support for openff-bespokefit

  #262 opened 8 months ago by jmichel80
  9

• [BUG] Gromacs `FreeEnergyMinimisation` and `FreeEnergyEquilibration` failing when using `restraint`

  #339 opened 2 months ago by mb2055
  7

• [BUG] Failure to run when minimising with restraints using `OpenMM`

  #340 opened 2 months ago by mb2055
  3

• [BUG] system.updateMolecules() doesn't work correctly for multiple molecules

  #335 opened 2 months ago by lohedges
  0

• [BUG] Unable to align based on single atom mappings

  #332 opened 3 months ago by lohedges
  0

• Question about ABFE using restraint search

  #329 opened 3 months ago by jnutyj
  13

• [BUG] BSS.Convert.toRDKit() appears to lose stereochemical information

  #330 opened 3 months ago by noahharrison64
  9

• runtime error

  #317 opened 4 months ago by mayank-kohli
  16

• Prepare systems with multiple ligands

  #326 opened 4 months ago by cespos
  9

• jaxlib incompatibility with a fresh bss install

  #296 opened 4 months ago by jmichel80
  6

• Customizing the gmx mdrun Parameters

  #316 opened 4 months ago by ErikZhang-9762
  2

• ABFE tutorial question

  #325 opened 4 months ago by jnutyj
  2

• [BUG] BioSimSpace.FreeEnergy.engines() doesn't report AMBER as an option

  #322 opened 4 months ago by lohedges
  0

• [BUG] Process.Somd is missing the extra_args kwarg

  #318 opened 4 months ago by lohedges
  0

• error during restraint search

  #315 opened 4 months ago by mayank-kohli
  6

• [BUG] Unable to merge ions

  #312 opened 4 months ago by lohedges
  0

• [BUG] Dummy atom atomtypes are no longer written to GROMACS topology files

  #306 opened 5 months ago by akalpokas
  3

• [BUG] Docstrings for ROI parameters

  #304 opened 5 months ago by akalpokas
  1

• [BUG] Unable to save Mol2 files through BioSimSpace

  #299 opened 5 months ago by lohedges
  6

• [BUG] Incorrect return type in BioSimSpace.Parameters funciton docstrings

  #297 opened 5 months ago by lohedges
  0

• How to copy the coordinates from a non-parameterised molecules to a parameterised molecule which has no coordinates

  #268 opened 7 months ago by DreamCykl
  18

• [BUG] prepareFEP.py calls `BSS.IO.saveMolecules` with an missing `match_water` parameter

  #291 opened 6 months ago by nigel-palmer-cresset
  2

• Option to write parameterisation intermediary file in SDF format to retain bond information

  #284 opened 6 months ago by noahharrison64
  11

• [BUG] Dummy atoms not detected during pert file writing when system created via sire.morph.create_from_pertfile

  #288 opened 6 months ago by lohedges
  0

• [BUG] Internal trajectory frame coordinate file might have inconsistent numbering with the system topology

  #285 opened 7 months ago by lohedges
  0

• [BUG] Trajectory.getFrames assumes system fileformat property is iterable

  #282 opened 7 months ago by lohedges
  0

• [BUG] getFrame space check incorrecty uses self

  #280 opened 7 months ago by lohedges
  0

• [BUG] Protocol.Metadynamics is missing the thermostat_time_constant option

  #275 opened 7 months ago by lohedges
  0

• [BUG] fileformat property no longer preserved when converting a molecule to a system

  #273 opened 7 months ago by lohedges
  0

• [BUG] The base Protocol should return None for getRestraint

  #274 opened 7 months ago by lohedges
  0

• [BUG] Non-reproducible search for restraint atoms

  #270 opened 8 months ago by lohedges
  0

• [BUG] Potential memory leak when saving systems

  #265 opened 8 months ago by noahharrison64
  5

• [BUG] Ions should be excluded in AMBER position restraint mask

  #258 opened 8 months ago by lohedges
  0

• [BUG] The __pow__ operator for BioSimSpace.Types._GeneralUnit doesn't handle fractional exponents

  #259 opened 8 months ago by lohedges
  0

• [BUG] GROMACS hybrid topology file is lost when protocol used position restraints

  #256 opened 8 months ago by lohedges
  0

• 'is_crystal' prevents setup for GROMACS Relative Free Energy files

  #261 opened 9 months ago by annamherz
  3

• [BUG] Improve error message when attempting to extract selection that only contains dummies

  #250 opened 9 months ago by lohedges
  0

• Add a flag to BSS.Align.decouple to only change the sire property when using this for SOMD

  #252 opened 9 months ago by xiki-tempula
  4

• [BUG]Is there a bug for funnel correction when estimating the average area of the restraint?

  #246 opened 9 months ago by zheqiang-zhong
  1

• [BUG] System instantiation fails is perturbed system is missing molecule0 or molecule1 properties

  #248 opened 9 months ago by lohedges
  0

• [BUG] readPerturbableSystem needs to remove shared system properties

  #241 opened 9 months ago by lohedges
  0

• [BUG] OpenFF parameterisation error reports the incorrect file name.

  #242 opened 9 months ago by lohedges
  0

• [BUG] Expose FreeEnergyMixin protocols for GROMACS

  #243 opened 9 months ago by lohedges
  0