|
About pmx: Automated protein structure and topology generation for alchemical perturbations
|
|
0
|
1254
|
June 10, 2016
|
|
Bonds that rotated more than 30 degrees:
|
|
1
|
45
|
November 3, 2022
|
|
IndexError: list index out of range while preparing pdb file
|
|
1
|
115
|
September 15, 2022
|
|
Problem with installing with Python2
|
|
9
|
41
|
September 7, 2022
|
|
Ligand topolgies for pmx
|
|
5
|
90
|
September 1, 2022
|
|
Pmx RBFE gives oddly large deltaG
|
|
1
|
65
|
August 14, 2022
|
|
PMX engineered resiude
|
|
4
|
84
|
July 18, 2022
|
|
Pmx ABFE ligand only simulation set-up
|
|
3
|
95
|
July 18, 2022
|
|
Using pmx genlib and hybrid topologies
|
|
3
|
103
|
July 11, 2022
|
|
PMX generating protein ligand simulation system with Charmm/cgenff forcefields
|
|
1
|
118
|
June 14, 2022
|
|
Free energy calculations error
|
|
1
|
263
|
June 14, 2022
|
|
Free Energy Calculation: State B has non-zero total charge: -1.000000
|
|
1
|
110
|
June 14, 2022
|
|
Free energy calculation with double system/single box simulation
|
|
12
|
183
|
March 30, 2022
|
|
Error with Zn atom
|
|
3
|
129
|
March 29, 2022
|
|
Problem with SS bridges - Bug?
|
|
3
|
119
|
March 24, 2022
|
|
Peptide Nucleic Acid Functionality
|
|
2
|
164
|
January 2, 2022
|
|
Pmx - problems reproducing benchmarking from de Groot 2020
|
|
2
|
246
|
October 17, 2021
|
|
Itp ligand file generation
|
|
3
|
465
|
October 14, 2021
|
|
A non-finite potential energy in non-equilibrium transition with pmx
|
|
2
|
268
|
October 1, 2021
|
|
Alchemical free energy calculations
|
|
1
|
238
|
October 1, 2021
|
|
LINCS error during Alchemical free energy calculation
|
|
1
|
243
|
September 30, 2021
|
|
Energy minimization of hybrid ligand
|
|
2
|
353
|
November 13, 2020
|
|
Relative constraint deviation after LINCS
|
|
6
|
1127
|
October 9, 2020
|
|
Dual Topology Generator for Alchemical Pathways
|
|
1
|
553
|
October 9, 2020
|
|
Make_hybrid.py list index out of range error
|
|
2
|
432
|
October 9, 2020
|
|
Installed - can't import _pmx as _p
|
|
3
|
649
|
July 4, 2020
|
|
Follow-Up from Webinar: Mutation free energy calculations with pmx
|
|
0
|
1291
|
June 10, 2016
|