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openmm
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pdbfixer
PDBFixer fixes problems in PDB files
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fix CI badge; remove some old simtk
#246
dwhswenson
closed
2 years ago
1
Added boxShape option to addSolvent()
#245
peastman
closed
2 years ago
0
No matching distribution found for openmm>=7.1 (from pdbfixer)
#244
tkcaccia
closed
2 years ago
2
How to eliminate hydrogen
#243
yhgon
closed
2 years ago
4
Potential Energy mantisa is same for all iteration.
#242
yhgon
closed
2 years ago
2
one case cannot fix missing residue
#241
yhgon
closed
2 years ago
4
question for PDBFixer
#240
yhgon
closed
2 years ago
2
Updated manual to show current output of --help
#239
peastman
closed
2 years ago
0
User manual not updated
#238
BJWiley233
closed
2 years ago
1
PDB file lines read in as Models, throws "AttributeError: 'Model' object has no attribute 'decode'"
#237
ddcas9
opened
2 years ago
5
Rename chain
#236
IkramMHD
closed
2 years ago
2
Fix DeprecationWarning (#233)
#235
jnooree
closed
2 years ago
1
phosaa14SB.xml KeyError and Resolution
#234
jhmlam
closed
2 years ago
2
PDBFixer issue (Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.)
#233
markuslacher
closed
2 years ago
0
Index out of bounds error when calling fixer function
#232
Tonylac77
closed
2 years ago
3
Is bond order available via pdbfixer?
#231
ljmartin
closed
2 years ago
3
PDBFixer is changing chain names
#230
raoufkeskes
opened
2 years ago
1
Updated version number to 1.8.1
#229
peastman
closed
2 years ago
0
Fixed error leading to duplicate bonds
#228
peastman
closed
2 years ago
1
PDBFixer not working some PDB file
#227
AhmetGG
opened
2 years ago
5
Fix typos discovered by codespell
#226
cclauss
closed
2 years ago
3
Revamp PDBFixer testing
#225
swails
closed
2 years ago
5
Convert to GitHub actions to re-enable continuous integration
#224
jchodera
closed
2 years ago
1
Changes to work with OpenMM 7.6
#223
peastman
closed
2 years ago
0
GitHub Action to lint Python code
#222
cclauss
closed
2 years ago
14
Fix reading PDBx from filename
#221
dww100
closed
3 years ago
1
addMissingAtoms() adds a linear chain of residues to protein termini in PDB ID 2a07
#220
lancelot-droid
closed
3 years ago
4
PDBs from RCSB failed to reconstruct
#219
slawek111
opened
3 years ago
7
how to handle non standard amino acids e.g. PTR
#218
michelsanner
opened
3 years ago
5
Documentation needed?
#217
Leo-Ryu
closed
3 years ago
1
Updated version in setup.py
#216
peastman
closed
3 years ago
0
Support all lipid types from OpenMM 7.5
#215
peastman
closed
3 years ago
0
Fixed 'See our manual' link
#214
TrianguloY
closed
3 years ago
1
After fixing my protein giving long tail
#213
Bio-Otto
closed
3 years ago
3
See our manual link broken
#212
birbilis
closed
3 years ago
11
Fix Travis builds
#211
peastman
closed
3 years ago
1
Charges lost on ASP and GLU residues
#210
tdudgeon
opened
3 years ago
1
Histidines created with Hs at HD1 and HE1
#209
tdudgeon
closed
3 years ago
2
Fixed box vectors for truncated octahedron
#208
peastman
closed
3 years ago
2
combining fixed PDBs
#207
michelsanner
closed
3 years ago
2
Maintain wanted heterogens
#206
ghost
opened
3 years ago
4
How to select a single position for atoms with multiple alternate positions listed
#205
ghost
opened
3 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
opened
4 years ago
2
Added option to save files in PDBx/mmCIF format
#197
peastman
closed
4 years ago
0
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