|
About pmx: Automated protein structure and topology generation for alchemical perturbations
|
|
0
|
1603
|
June 10, 2016
|
|
Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
|
|
1
|
12
|
November 13, 2025
|
|
Absolute binding Free energy with NE-MD: Single-step complex leg & Boresch restraint tips
|
|
1
|
49
|
August 4, 2025
|
|
Issue in Probability distribution overlap for D2E transformation
|
|
8
|
45
|
July 4, 2025
|
|
Challenges in Reproducing ddG Estimation Results for 1STN
|
|
28
|
464
|
June 5, 2025
|
|
Mutation free energy calculation for protein membrane interaction
|
|
2
|
44
|
May 19, 2025
|
|
Repeatability of state A to State B alchemical transformation
|
|
2
|
43
|
April 17, 2025
|
|
PMX alchemical free energy calculation for protein mutation
|
|
1
|
62
|
March 25, 2025
|
|
Pmx ligandHybrid error
|
|
7
|
81
|
March 15, 2025
|
|
PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies
|
|
2
|
60
|
February 28, 2025
|
|
Error with pmx and openforcefield generated files
|
|
1
|
59
|
January 27, 2025
|
|
Pmx and CHARM36 using output from CGenFF server
|
|
3
|
50
|
January 20, 2025
|
|
Pmx analyse says "no good dgdl files provided"
|
|
2
|
24
|
January 13, 2025
|
|
Installation Problem of PMX
|
|
12
|
111
|
January 13, 2025
|
|
Help request protein-ligand tutorial error fix
|
|
8
|
72
|
December 30, 2024
|
|
Help with Charged Ligand Non-Equilibrium Free Energy Calculations Using Co-Alchemical Ion Approach
|
|
3
|
70
|
December 20, 2024
|
|
Relative constraint deviation after LINCS
|
|
15
|
2234
|
December 9, 2024
|
|
LINCS warning and segmentation fault @ non-equilibrium part of simulation
|
|
7
|
89
|
December 9, 2024
|
|
PMX AssertionError, Atom type OH not been defined in the force field, Atom DHD1 was not found
|
|
3
|
51
|
November 13, 2024
|
|
After running the ddG calculation tutorial (ligand_tutorial.ipynb), I got different result
|
|
7
|
89
|
October 28, 2024
|
|
Non-standard amino acid mutation - dihedrals error
|
|
2
|
65
|
September 25, 2024
|
|
Is the pmx web-server OK?
|
|
1
|
30
|
September 25, 2024
|
|
Pmx and protein structure water molecules
|
|
2
|
72
|
May 24, 2024
|
|
Error in AtomMapping with more than 100 atoms
|
|
2
|
89
|
April 4, 2024
|
|
Pmx error pmx mutate -f protein.pdb -o mutant.pdb
|
|
1
|
192
|
March 6, 2024
|
|
'ligandHybrid' ERROR: fitting mol2 on mol1 failed
|
|
4
|
191
|
February 21, 2024
|
|
LINCS constraints all bonds to h-bonds only
|
|
7
|
153
|
February 16, 2024
|
|
Error with 'make_hybrid.py' Using CGenFF
|
|
4
|
158
|
February 12, 2024
|
|
Issue with pdb2gmx and charm36mut forcefield: Undefined Atom Type "OH"
|
|
4
|
382
|
December 7, 2023
|
|
Make_hybrid.py list index out of range error
|
|
14
|
1169
|
December 4, 2023
|