OpenBioSim/biosimspace

Issues

• Question about ABFE using restraint search

  #329 opened a month ago by jnutyj
  13

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

  #330 opened a month ago by noahharrison64
  9

• runtime error

  #317 opened a month ago by mayank-kohli
  16

• Prepare systems with multiple ligands

  #326 opened a month ago by cespos
  9

• jaxlib incompatibility with a fresh bss install

  #296 opened a month ago by jmichel80
  6

• Customizing the gmx mdrun Parameters

  #316 opened a month ago by ErikZhang-9762
  2

• ABFE tutorial question

  #325 opened a month ago by jnutyj
  2

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

  #322 opened a month ago by lohedges
  0

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

  #318 opened 2 months ago by lohedges
  0

• error during restraint search

  #315 opened 2 months ago by mayank-kohli
  6

• [BUG] Unable to merge ions

  #312 opened 2 months ago by lohedges
  0

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

  #306 opened 3 months ago by akalpokas
  3

• [BUG] Docstrings for ROI parameters

  #304 opened 3 months ago by akalpokas
  1

• [BUG] Unable to save Mol2 files through BioSimSpace

  #299 opened 3 months ago by lohedges
  6

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

  #297 opened 3 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 5 months ago by DreamCykl
  18

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

  #291 opened 4 months ago by nigel-palmer-cresset
  2

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

  #284 opened 4 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 4 months ago by lohedges
  0

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

  #285 opened 4 months ago by lohedges
  0

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

  #282 opened 4 months ago by lohedges
  0

• [BUG] getFrame space check incorrecty uses self

  #280 opened 4 months ago by lohedges
  0

• Support for openff-bespokefit

  #262 opened 6 months ago by jmichel80
  0

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

  #275 opened 5 months ago by lohedges
  0

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

  #273 opened 5 months ago by lohedges
  0

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

  #274 opened 5 months ago by lohedges
  0

• [BUG] Non-reproducible search for restraint atoms

  #270 opened 5 months ago by lohedges
  0

• [BUG] Potential memory leak when saving systems

  #265 opened 6 months ago by noahharrison64
  5

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

  #258 opened 6 months ago by lohedges
  0

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

  #259 opened 6 months ago by lohedges
  0

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

  #256 opened 6 months ago by lohedges
  0

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

  #261 opened 6 months ago by annamherz
  3

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

  #250 opened 7 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 7 months ago by xiki-tempula
  4

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

  #246 opened 7 months ago by zheqiang-zhong
  1

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

  #248 opened 7 months ago by lohedges
  0

• Unable to parameterise with OFF2

  #240 opened 7 months ago by fjclark
  8

• [BUG] readPerturbableSystem needs to remove shared system properties

  #241 opened 7 months ago by lohedges
  0

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

  #242 opened 7 months ago by lohedges
  0

• [BUG] Expose FreeEnergyMixin protocols for GROMACS

  #243 opened 7 months ago by lohedges
  0

• reduceBoxVectors does not prevent RuntimeError: Periodic box vectors must be in reduced form

  #238 opened 7 months ago by fjclark
  14

• [BUG] GROMACS specific options are only applied for lambda=0 window when setup_only=True

  #236 opened 7 months ago by lohedges
  0

• [BUG] generateNetwork raises TypeError when links_file is supplied

  #231 opened 8 months ago by jasmin-guven
  3

• [BUG] Strange logging behaviour

  #232 opened 8 months ago by noahharrison64
  6

• Conda Installation of Dev Version Fails

  #229 opened 8 months ago by fjclark
  5

• [BUG] custom_parameters option not exposed via AMBER protein force field generator

  #225 opened 9 months ago by lohedges
  1

• [BUG] Disulphide bond code fails when a single bond is present

  #223 opened 9 months ago by lohedges
  1

• [BUG] AMBER restraint mask needs to match all hydrogens, not just those named H

  #221 opened 9 months ago by lohedges
  0

• [BUG] process.getTrajectory() not swapping backend if one was already specified

  #218 opened 9 months ago by lohedges
  0

• [BUG] Funnel metadynamics tutorial fails due to duplicate default force constants

  #216 opened 9 months ago by lohedges
  5