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OpenBioSim
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biosimspace
An interoperable Python framework for biomolecular simulation.
https://biosimspace.openbiosim.org
GNU General Public License v3.0
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Fix issue #330
#331
lohedges
opened
2 weeks ago
4
[BUG] BSS.Convert.toRDKit() appears to lose stereochemical information
#330
noahharrison64
opened
2 weeks ago
9
Question about ABFE using restraint search
#329
jnutyj
closed
3 weeks ago
13
Alchemical Transfer Method
#327
mb2055
opened
4 weeks ago
0
Prepare systems with multiple ligands
#326
cespos
opened
1 month ago
9
ABFE tutorial question
#325
jnutyj
closed
1 month ago
2
Backport fix from PR #323 into main
#324
lohedges
closed
1 month ago
0
Fix issue #322
#323
lohedges
closed
1 month ago
1
[BUG] BioSimSpace.FreeEnergy.engines() doesn't report AMBER as an option
#322
lohedges
closed
1 month ago
0
Backport fix from #319 into main
#321
lohedges
closed
1 month ago
0
Fix issue #318
#319
lohedges
closed
1 month ago
0
[BUG] Process.Somd is missing the extra_args kwarg
#318
lohedges
closed
1 month ago
0
runtime error
#317
mayank-kohli
closed
4 weeks ago
16
Customizing the gmx mdrun Parameters
#316
ErikZhang-9762
closed
1 month ago
2
error during restraint search
#315
mayank-kohli
closed
1 month ago
6
Backport fixes from #313
#314
lohedges
closed
1 month ago
0
Fix issue #312
#313
lohedges
closed
1 month ago
4
[BUG] Unable to merge ions
#312
lohedges
closed
1 month ago
0
Backport fix from PR #310
#311
lohedges
closed
1 month ago
0
Update PFEP Tutorial Link
#310
akalpokas
closed
1 month ago
2
Add Protein FEP tutorial
#309
akalpokas
closed
1 month ago
3
Release 2024.2.0
#308
lohedges
closed
1 month ago
1
Synchronise with Exscientia remote
#307
lohedges
closed
2 months ago
2
[BUG] Dummy atom atomtypes are no longer written to GROMACS topology files
#306
akalpokas
closed
2 months ago
3
Fix align function docstrings [ci skip]
#305
akalpokas
closed
2 months ago
0
[BUG] Docstrings for ROI parameters
#304
akalpokas
closed
2 months ago
1
Backport fix from PR #302
#303
lohedges
closed
2 months ago
0
Expose torsion modification kwargs
#302
lohedges
closed
2 months ago
0
Backport fixes from #295, #298, and #300
#301
lohedges
closed
2 months ago
0
Fix issue #299
#300
lohedges
closed
2 months ago
4
[BUG] Unable to save Mol2 files through BioSimSpace
#299
lohedges
closed
2 months ago
6
Fix issue #297
#298
lohedges
closed
2 months ago
0
[BUG] Incorrect return type in BioSimSpace.Parameters funciton docstrings
#297
lohedges
closed
2 months ago
0
jaxlib incompatibility with a fresh bss install
#296
jmichel80
closed
1 month ago
6
Don't perturb LJ sigma for ghost atoms
#295
lohedges
closed
2 months ago
10
Add Protein FEP Functionality
#294
akalpokas
closed
2 months ago
11
Backport fixes from PR #292
#293
lohedges
closed
3 months ago
0
Fix issue #291
#292
lohedges
closed
3 months ago
1
[BUG] prepareFEP.py calls `BSS.IO.saveMolecules` with an missing `match_water` parameter
#291
nigel-palmer-cresset
closed
3 months ago
2
Backport fixes from PR #287 and #289
#290
lohedges
closed
3 months ago
0
Fix issue #288
#289
lohedges
closed
3 months ago
0
[BUG] Dummy atoms not detected during pert file writing when system created via sire.morph.create_from_pertfile
#288
lohedges
closed
3 months ago
0
Fix issue #284
#287
lohedges
closed
3 months ago
0
Backport fix from PR #281 into main
#286
lohedges
closed
4 months ago
0
[BUG] Internal trajectory frame coordinate file might have inconsistent numbering with the system topology
#285
lohedges
closed
4 months ago
0
Option to write parameterisation intermediary file in SDF format to retain bond information
#284
noahharrison64
closed
3 months ago
11
Fix Trajectory object cannot handle system generated from file
#283
xiki-tempula
closed
4 months ago
0
[BUG] Trajectory.getFrames assumes system fileformat property is iterable
#282
lohedges
closed
4 months ago
0
Fix issue #280
#281
lohedges
closed
4 months ago
13
[BUG] getFrame space check incorrecty uses self
#280
lohedges
closed
4 months ago
0
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