openmm/pdbfixer

Issues

• ACE ignored when calling addMissingHydrogens

  #319 opened a month ago by ross-pure
  4

• Remove use of cgi module

  #318 opened 2 months ago by peastman
  0

• Have removeHeterogens() return the toDelete[] list?

  #315 opened 2 months ago by Chance626
  5

• Enhancement requests if not already existing?

  #247 opened 2 months ago by BJWiley233
  5

• Adding phosphorylated residues to PDBFixer templates

  #259 opened 2 months ago by sukritsingh
  13

• Residues are not recorded correctly

  #260 opened 2 months ago by Ruibin-Liu
  1

• [Unexpected behaviour] Unexpected behavoiur when parsing mmCIF files

  #269 opened 2 months ago by Croydon-Brixton
  5

• Is there any molecular dynamics or docking research published using pdbfixer?

  #270 opened 2 months ago by RuikangSun
  5

• Invalide chirality when fixing neural network generated structure

  #274 opened 2 months ago by ryankzhu
  3

• pH protonation valid

  #278 opened 2 months ago by groponp
  1

• findMissingAtoms raises AttributeError if findMissingResidues has not been called first

  #279 opened 2 months ago by nielskm
  1

• Mutating to non-standard amino acids not present in available force field libraries

  #286 opened 2 months ago by amin-sagar
  5

• How can I cite this tool if I use it

  #288 opened 2 months ago by tang2552
  1

• openmm.OpenMMException: Particle coordinate is nan

  #289 opened 2 months ago by VeScarecrow
  3

• `PDBFixer.addSolvent` often incorrectly neutralises systems with charged ligands as though they were neutral

  #299 opened 2 months ago by Yoshanuikabundi
  8

• fixer.findMissingResidues() could not find the missing residues !

  #305 opened 2 months ago by Jalil-Mahdizadeh
  5

• pkg_resources is deprecated as an API

  #311 opened 2 months ago by kiyoon
  1

• pypi version

  #254 opened 2 years ago by Pantelispanka
  13

• PDBFixer - in some cases added residues have amides with non-trans OCNH stereochemistry

  #307 opened 3 months ago by ivanicj
  14

• Support for PDB files with multiple frames?

  #310 opened 3 months ago by jeevster
  2

• CASN adds hydrogenation errors

  #306 opened 3 months ago by astomer2
  5

• Weird coordinates and unable to add Hydrogens upon adding tyrosines

  #304 opened 4 months ago by sukritsingh
  5

• app.Modeller._loadStandardHydrogenDefinitions() AttributeError: type object 'Modeller' has no attribute '_loadStandardHydrogenDefinitions'

  #302 opened 5 months ago by MichaelAbel1
  2

• findMissingResidues does not detect residues missing from structure

  #300 opened 5 months ago by YoavShamir5
  10

• PDBFixer not writing out complete CONECT records for downloaded Templates

  #297 opened 6 months ago by sukritsingh
  10

• Error when having more than 10 chain identifiers

  #287 opened 6 months ago by FAOlivieri
  7

• Should PDBFixer write out SEQRES entries if provided in the input?

  #293 opened 7 months ago by sukritsingh
  9

• PDBFixer cannot handle nucleic acids with residue name N

  #281 opened a year ago by jamesmkrieger
  5

• PDBFixer adding repeated residues at the start.

  #291 opened 8 months ago by Ian-CP
  1

• Fixing out a very long chain with pdbfixer

  #290 opened 8 months ago by stan1233
  2

• mmCIF output - `_atom_site.label_entity_id` not written

  #285 opened a year ago by Augustin-Zidek
  1

• The repair of two ends of peptide didn't return the desired result

  #283 opened a year ago by bdx114514
  0

• How to avoid conflicts with other atoms of the protein when undergoing amino acid mutations?

  #282 opened a year ago by 9527567
  2

• Do we have method to mutate the iCode-containing residue?

  #280 opened a year ago by locitran
  2

• Processed Receptor has Long Legs in PDB File

  #276 opened a year ago by syedzayyan
  14

• Issue with Multiprocessing

  #277 opened a year ago by cplateVT
  10

• PDBFixer API cannot fix mmCIF file

  #275 opened a year ago by locitran
  5

• PDBfixer with python=3.10 and openmm=7.7

  #272 opened 2 years ago by matteo-cagiada
  2

• pdbfixer doesn

  #271 opened 2 years ago by matteo-cagiada
  0

• Select residue atom positions for residues with alternate locations (altloc)

  #253 opened 2 years ago by JSLJ23
  4

• For those care about the running time

  #264 opened 2 years ago by Minys233
  3

• Missing b factors

  #266 opened 2 years ago by zlcrrrr
  2

• `fixer.findMissingResidues()` fails on 3ODU

  #255 opened 2 years ago by JSLJ23
  2

• Failed to find missing residues in 6VYC

  #256 opened 2 years ago by jw-feng
  6

• Cannot add missing atoms

  #252 opened 2 years ago by kntkb
  2

• Which parameter set(periodicity, offset, k) does PeriodicTorsionForce use in soft.xml?

  #250 opened 2 years ago by psp3dcg
  8

• Adding two terminal caps to a single residue

  #251 opened 2 years ago by ljmartin
  2

• Version 1.8.1 fails to addSolvent() when boxShape kwarg is present. Also in openmm-setup

  #249 opened 3 years ago by pguillem
  2

• remove

  #248 opened 3 years ago by jaredsagendorf
  0

• No matching distribution found for openmm>=7.1 (from pdbfixer)

  #244 opened 3 years ago by tkcaccia
  2