|
PMX repeatability is very poor
|
|
8
|
289
|
April 4, 2023
|
|
Janssen Ligand tutorial: why no -H2Hpolar flag in atoms_to_morph.py?
|
|
1
|
265
|
March 22, 2023
|
|
AMBER99SB-ILDN warning alert
|
|
3
|
330
|
March 10, 2023
|
|
Understanding the options of atom mapping and ligandHybrid
|
|
57
|
696
|
February 23, 2023
|
|
Oscillational period warning during tripeptide A2I forward simulation
|
|
14
|
618
|
January 31, 2023
|
|
Problem in using gentop
|
|
12
|
315
|
January 20, 2023
|
|
List index out of range when running pmx gentop
|
|
2
|
323
|
December 29, 2022
|
|
Bonds that rotated more than 30 degrees:
|
|
1
|
376
|
November 3, 2022
|
|
IndexError: list index out of range while preparing pdb file
|
|
1
|
435
|
September 15, 2022
|
|
Ligand topolgies for pmx
|
|
5
|
527
|
September 1, 2022
|
|
Pmx RBFE gives oddly large deltaG
|
|
1
|
386
|
August 14, 2022
|
|
PMX engineered resiude
|
|
4
|
284
|
July 18, 2022
|
|
Pmx ABFE ligand only simulation set-up
|
|
3
|
478
|
July 18, 2022
|
|
Using pmx genlib and hybrid topologies
|
|
3
|
509
|
July 11, 2022
|
|
PMX generating protein ligand simulation system with Charmm/cgenff forcefields
|
|
1
|
481
|
June 14, 2022
|
|
Free energy calculations error
|
|
1
|
1540
|
June 14, 2022
|
|
Free Energy Calculation: State B has non-zero total charge: -1.000000
|
|
1
|
404
|
June 14, 2022
|
|
Free energy calculation with double system/single box simulation
|
|
12
|
531
|
March 30, 2022
|
|
Error with Zn atom
|
|
3
|
419
|
March 29, 2022
|
|
Problem with SS bridges - Bug?
|
|
3
|
327
|
March 24, 2022
|
|
Peptide Nucleic Acid Functionality
|
|
2
|
425
|
January 2, 2022
|
|
Pmx - problems reproducing benchmarking from de Groot 2020
|
|
2
|
673
|
October 17, 2021
|
|
Itp ligand file generation
|
|
3
|
980
|
October 14, 2021
|
|
A non-finite potential energy in non-equilibrium transition with pmx
|
|
2
|
476
|
October 1, 2021
|
|
Alchemical free energy calculations
|
|
1
|
451
|
October 1, 2021
|
|
LINCS error during Alchemical free energy calculation
|
|
1
|
555
|
September 30, 2021
|
|
Energy minimization of hybrid ligand
|
|
2
|
569
|
November 13, 2020
|
|
Relative constraint deviation after LINCS
|
|
6
|
2118
|
October 9, 2020
|
|
Dual Topology Generator for Alchemical Pathways
|
|
1
|
820
|
October 9, 2020
|
|
Installed - can't import _pmx as _p
|
|
3
|
1020
|
July 4, 2020
|