openmm pdbfixer issues - Githubissues

openmm / pdbfixer

PDBFixer fixes problems in PDB files

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Remove use of cgi module

#318 peastman opened 2 weeks ago
0
CI tests against the released OpenMM

#317 peastman closed 2 weeks ago
0
removeHeterogens() returns the Residues that were removed

#316 peastman closed 3 weeks ago
0
Have removeHeterogens() return the toDelete[] list?

#315 Chance626 closed 3 weeks ago
5
Update version numbers

#314 peastman closed 2 weeks ago
0
membraneCenterZ was being ignored

#313 peastman closed 1 month ago
0
Removed a deprecated import

#312 peastman closed 1 month ago
0
pkg_resources is deprecated as an API

#311 kiyoon closed 1 month ago
1
Support for PDB files with multiple frames?

#310 jeevster closed 1 month ago
2
Try to put peptide bonds in the correct orientation

#309 peastman closed 1 month ago
0
Soft core force field includes torsions with wildcards

#308 peastman closed 1 month ago
1
PDBFixer - in some cases added residues have amides with non-trans OCNH stereochemistry

#307 ivanicj opened 1 month ago
14
CASN adds hydrogenation errors

#306 astomer2 closed 2 months ago
5
fixer.findMissingResidues() could not find the missing residues !

#305 Jalil-Mahdizadeh closed 4 weeks ago
5
Weird coordinates and unable to add Hydrogens upon adding tyrosines

#304 sukritsingh opened 3 months ago
5
Added optimizeHydrogenBonds()

#303 peastman opened 3 months ago
0
app.Modeller._loadStandardHydrogenDefinitions() AttributeError: type object 'Modeller' has no attribute '_loadStandardHydrogenDefinitions'

#302 MichaelAbel1 closed 3 months ago
2
Neutralise systems with formal charges from the PDB

#301 Yoshanuikabundi closed 2 months ago
8
findMissingResidues does not detect residues missing from structure

#300 YoavShamir5 closed 4 months ago
10
`PDBFixer.addSolvent` often incorrectly neutralises systems with charged ligands as though they were neutral

#299 Yoshanuikabundi closed 4 weeks ago
8
Fixed bug in added bonds to heterogens

#298 peastman closed 4 months ago
1
PDBFixer not writing out complete CONECT records for downloaded Templates

#297 sukritsingh closed 4 months ago
10
Support nonstandard residues

#296 peastman closed 4 months ago
0
Can add hydrogens to nonstandard residues

#295 peastman closed 4 months ago
1
Bugfixed chain ID assignment in addSolvent (#287)

#294 murfalo closed 5 months ago
5
Should PDBFixer write out SEQRES entries if provided in the input?

#293 sukritsingh opened 5 months ago
9
[bug] Ensure numpy < 2 version

#292 awlange closed 5 months ago
3
PDBFixer adding repeated residues at the start.

#291 Ian-CP closed 6 months ago
1
Fixing out a very long chain with pdbfixer

#290 stan1233 closed 7 months ago
2
openmm.OpenMMException: Particle coordinate is nan

#289 VeScarecrow closed 4 weeks ago
3
How can I cite this tool if I use it

#288 tang2552 closed 4 weeks ago
1
Error when having more than 10 chain identifiers

#287 FAOlivieri closed 5 months ago
7
Mutating to non-standard amino acids not present in available force field libraries

#286 amin-sagar closed 4 weeks ago
5
mmCIF output - `_atom_site.label_entity_id` not written

#285 Augustin-Zidek closed 10 months ago
1
fix add missing unknown (UNK) residues error

#284 ndonyapour opened 11 months ago
3
The repair of two ends of peptide didn't return the desired result

#283 bdx114514 opened 11 months ago
0
How to avoid conflicts with other atoms of the protein when undergoing amino acid mutations?

#282 9527567 closed 12 months ago
2
PDBFixer cannot handle nucleic acids with residue name N

#281 jamesmkrieger opened 1 year ago
5
Do we have method to mutate the iCode-containing residue?

#280 locitran opened 1 year ago
2
findMissingAtoms raises AttributeError if findMissingResidues has not been called first

#279 nielskm closed 4 weeks ago
1
pH protonation valid

#278 groponp closed 4 weeks ago
1
Issue with Multiprocessing

#277 cplateVT closed 1 year ago
10
Processed Receptor has Long Legs in PDB File

#276 syedzayyan closed 1 year ago
14
PDBFixer API cannot fix mmCIF file

#275 locitran closed 1 year ago
5
Invalide chirality when fixing neural network generated structure

#274 ryankzhu closed 4 weeks ago
3
Updated version number to 1.9

#273 peastman closed 1 year ago
0
PDBfixer with python=3.10 and openmm=7.7

#272 matteo-cagiada closed 1 year ago
2
pdbfixer doesn

#271 matteo-cagiada closed 1 year ago
0
Is there any molecular dynamics or docking research published using pdbfixer?

#270 RuikangSun closed 4 weeks ago
5
[Unexpected behaviour] Unexpected behavoiur when parsing mmCIF files

#269 Croydon-Brixton closed 4 weeks ago
5