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Electrostatics
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pdb2pqr
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Failing with over 99999 atoms.
#288
jacob-r-anderson
closed
2 years ago
6
Remove the temporary pdb file written for propka
#286
stefdoerr
closed
2 years ago
1
PDB2PQR not working with 4E8P and 6T3R
#283
sobolevnrm
closed
2 years ago
5
Version 3.5.0
#282
sobolevnrm
closed
2 years ago
1
Add more broken backbone tests
#281
sobolevnrm
closed
2 years ago
1
Document limitation of a single ligand in calculations
#280
sobolevnrm
closed
2 years ago
1
Add (optional) long tests for more thorough testing
#279
sobolevnrm
closed
2 years ago
2
Need testing of various command-line options
#278
sobolevnrm
opened
2 years ago
0
Investigate broken tests
#277
sobolevnrm
closed
2 years ago
3
Add NGL to list of recommended visualization tools.
#276
sobolevnrm
closed
2 years ago
1
Choose best hydrogen bonds for non-bonded atom.
#275
sobolevnrm
closed
2 years ago
1
Update PyPI setup for Markdown content.
#274
sobolevnrm
closed
2 years ago
1
Improve error messages related to MOL2 bond types
#273
sobolevnrm
closed
2 years ago
1
Remove-non functional psize command line code.
#272
sobolevnrm
closed
2 years ago
1
Add alternate name for serine atom and some output for troubleshooting charge issues
#271
sobolevnrm
closed
2 years ago
1
Standardize calculation of non-integer charges.
#270
sobolevnrm
closed
2 years ago
1
Fix problem with missing atoms in RNA.
#269
sobolevnrm
closed
2 years ago
1
Fix missing heavy atoms issue with RNA
#268
sobolevnrm
closed
2 years ago
1
PDB2PQR incorrectly reconstructing missing atoms in 4E8M
#267
sobolevnrm
closed
2 years ago
0
Fix incorrect integer charge check.
#266
sobolevnrm
closed
2 years ago
1
Remove excessive warnings about tetrahedral hydrogens.
#265
sobolevnrm
closed
2 years ago
1
Non-integer charge calculated incorrectly
#264
sobolevnrm
closed
2 years ago
0
Nathan/issue 262
#263
sobolevnrm
closed
2 years ago
1
Should be raising errors rather than returning 1
#262
sobolevnrm
closed
2 years ago
0
Version 3.4.1
#261
sobolevnrm
closed
2 years ago
1
Fix error in topology of ASN HD21 and HD22
#260
sobolevnrm
closed
2 years ago
1
v3.4.0
#259
sobolevnrm
closed
2 years ago
1
Fix issue with wrong pkas assigned to terminal residues
#258
stefdoerr
closed
2 years ago
3
Terminal histidine protonation issues
#257
stefdoerr
closed
2 years ago
2
PDB2PQR fails on files with only nucleic acid resides
#256
sobolevnrm
closed
2 years ago
6
Fixed calculation for grid lengths in psize
#255
intendo
closed
2 years ago
3
psize does not take into account HETATMs correctly
#254
intendo
closed
2 years ago
0
Check and possibly disable "tetrahedral hydrogen warning messages
#253
sobolevnrm
closed
2 years ago
0
Version 3.3.2
#252
sobolevnrm
closed
2 years ago
1
Fixes #250
#251
sobolevnrm
closed
2 years ago
1
pdb files with >999 residues are not processed correctly
#250
RayHackett
closed
2 years ago
13
Fixing rng seed for pdb2pqr tests
#249
stefdoerr
closed
2 years ago
7
Add PDB2PQR 3.3.1 to web server
#248
sobolevnrm
closed
2 years ago
2
Generate conda release for PDB2PQR 3.3.1
#247
sobolevnrm
closed
2 years ago
1
Nathan/v3.3.0
#246
sobolevnrm
closed
2 years ago
1
[BugReport] Titration state missing for N-ter/C-ter HIS
#245
shaoqx
closed
2 years ago
6
Extending PARSE and AMBER FF for non-standard amino-acids
#243
stefdoerr
closed
2 years ago
2
Swapped HD21/HD22 assignment for ASN
#242
chemsh
closed
2 years ago
3
Update aa.py
#241
intendo
closed
2 years ago
0
Wrong multi-line error strings
#240
stefdoerr
closed
2 years ago
0
Close dangling file pointer
#239
stefdoerr
closed
2 years ago
0
Allow users to disable protonation on specific residues
#238
stefdoerr
closed
2 years ago
1
Close dangling file pointer
#237
stefdoerr
closed
2 years ago
2
Error running pdb2pqr with PyMol
#236
mishaguy
closed
2 years ago
8
change per residue integer charge check to total charge interger chec…
#234
rkretsch
closed
2 years ago
2
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