issues
search
openmm
/
pdbfixer
PDBFixer fixes problems in PDB files
Other
453
stars
114
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
How to select a single position for atoms with multiple alternate positions listed
#205
ghost
opened
4 years ago
3
Which force field is used and how to change?
#204
CryoSky
closed
4 years ago
2
Python API: Keep chain
#203
mirix
opened
4 years ago
4
Problem with mmcif format
#202
georopon
closed
3 years ago
2
Residue number strange behavior
#201
MauriceKarrenbrock
opened
4 years ago
2
Trying to create SystemGenerator from RDKit converted openff topology
#200
tarungog
closed
4 years ago
3
List of fixes for failing test cases
#199
zhang-ivy
opened
4 years ago
2
[WIP] Improved method of selecting positions for added residues
#198
peastman
closed
2 weeks ago
2
Added option to save files in PDBx/mmCIF format
#197
peastman
closed
4 years ago
0
Move to openmm org?
#196
jchodera
closed
4 years ago
1
output mmCIF doesn't distinguish ATOMs from HETATMs and _atom_site.label_asym_id is overwritten by _atom_site.auth_asym_id
#195
MauriceKarrenbrock
closed
4 years ago
5
Missing terminal oxygen after addMissingAtoms()
#194
MauriceKarrenbrock
closed
4 years ago
17
MMCIF _atom_site.pdbx_PDB_ins_code problem
#193
MauriceKarrenbrock
closed
4 years ago
3
added Dockerfile; URL changed from `localhost` to `0.0.0.0`
#192
ozzzzz
closed
2 years ago
13
maintain insertion codes
#191
zhang-ivy
closed
4 years ago
1
Cannot find missing residues with "findMissingResidues"
#190
luwei0917
closed
4 years ago
6
Fixed exception loading PDBx/mmCIF files with missing blocks
#189
peastman
closed
4 years ago
0
PDBX/mmCIF reading error : asymIdCol = modData.getAttributeIndex('label_asym_id')
#188
MauriceKarrenbrock
closed
4 years ago
2
Insertion codes not preserved in addMissingAtoms
#187
zhang-ivy
closed
4 years ago
3
How to select a model?
#186
Ruibin-Liu
closed
4 years ago
1
Updated version number to 1.6
#185
peastman
closed
4 years ago
0
Improved handling of insertion codes
#184
peastman
closed
5 years ago
0
Fail to find missing residues on PDB retrieved from OPM database
#183
ajsilveira
opened
5 years ago
3
Make the addition of SEQRES residues optional
#182
jiayeguo
opened
5 years ago
3
wrong when install under CENTOS7
#181
guyujun
opened
5 years ago
2
Fixed error when calling _matchResidue(). OpenMM now uses compiled functions
#180
JoaoRodrigues
closed
5 years ago
6
Wrong placement of added hydrogens.
#179
niko97320
opened
5 years ago
9
Some bug fixes related to building missing residues
#178
nitroamos
opened
5 years ago
3
Added a seed parameter to addMissingAtoms to allow reproducible results
#177
JoaoRodrigues
closed
5 years ago
3
Non-reproducible behaviour of `addMissingAtoms`
#176
JoaoRodrigues
opened
5 years ago
0
pdbfixer is mislabeling built residues with negative res IDs
#175
nitroamos
opened
5 years ago
5
Update usage as "prog filename [options]"
#174
T-B-F
closed
5 years ago
1
best way to insert ACE/NME caps?
#173
nitroamos
opened
6 years ago
14
residue names based on protonation state?
#172
nitroamos
closed
6 years ago
2
Release 1.5
#171
jchodera
closed
6 years ago
2
More rigorous implementation of findMissingResidues needed (e.g., doesn't work for antibodies)
#170
nitroamos
opened
6 years ago
13
Short Script to equilibrate cells for systems created by in pdbfixer.
#169
ljmartin
closed
6 years ago
0
Fixed error when a file contains only one residue
#168
peastman
closed
6 years ago
0
ValueError in _findNearestDistance when protein has only one residue
#167
nitroamos
closed
6 years ago
0
Add Zenodo DOI?
#166
jchodera
opened
6 years ago
0
PDB clash pretty printer?
#165
nitroamos
closed
6 years ago
2
how to write pdb when resnum indices overflow the field width?
#164
nitroamos
closed
6 years ago
2
Exception: Particle coordinate is nan in addMembrane
#163
nitroamos
opened
6 years ago
6
wild/unminimized hydrogen placement
#162
nitroamos
closed
6 years ago
5
ZeroDivisionError: float division by zero
#161
nitroamos
closed
6 years ago
9
Add option for specifying platform (or platform name) to use?
#160
jchodera
closed
6 years ago
1
Solvent does not surround protein
#159
rnowling
closed
6 years ago
8
Update version number to 1.5
#158
peastman
closed
6 years ago
0
Can build membranes
#157
peastman
closed
6 years ago
6
Fixed error on files with only one chain
#156
peastman
closed
7 years ago
2
Previous
Next