|
About pmx: Automated protein structure and topology generation for alchemical perturbations
|
|
0
|
1556
|
June 10, 2016
|
|
Installation Problem of PMX
|
|
11
|
36
|
December 22, 2024
|
|
Help with Charged Ligand Non-Equilibrium Free Energy Calculations Using Co-Alchemical Ion Approach
|
|
3
|
7
|
December 20, 2024
|
|
Help request protein-ligand tutorial error fix
|
|
1
|
15
|
December 19, 2024
|
|
Relative constraint deviation after LINCS
|
|
15
|
2136
|
December 9, 2024
|
|
LINCS warning and segmentation fault @ non-equilibrium part of simulation
|
|
7
|
22
|
December 9, 2024
|
|
PMX AssertionError, Atom type OH not been defined in the force field, Atom DHD1 was not found
|
|
3
|
16
|
November 13, 2024
|
|
After running the ddG calculation tutorial (ligand_tutorial.ipynb), I got different result
|
|
7
|
23
|
October 28, 2024
|
|
Non-standard amino acid mutation - dihedrals error
|
|
2
|
35
|
September 25, 2024
|
|
Is the pmx web-server OK?
|
|
1
|
16
|
September 25, 2024
|
|
Pmx and protein structure water molecules
|
|
2
|
62
|
May 24, 2024
|
|
Challenges in Reproducing ddG Estimation Results for 1STN
|
|
27
|
328
|
April 19, 2024
|
|
Error in AtomMapping with more than 100 atoms
|
|
2
|
71
|
April 4, 2024
|
|
Pmx error pmx mutate -f protein.pdb -o mutant.pdb
|
|
1
|
157
|
March 6, 2024
|
|
'ligandHybrid' ERROR: fitting mol2 on mol1 failed
|
|
4
|
156
|
February 21, 2024
|
|
LINCS constraints all bonds to h-bonds only
|
|
7
|
136
|
February 16, 2024
|
|
Error with 'make_hybrid.py' Using CGenFF
|
|
4
|
134
|
February 12, 2024
|
|
Issue with pdb2gmx and charm36mut forcefield: Undefined Atom Type "OH"
|
|
4
|
276
|
December 7, 2023
|
|
Make_hybrid.py list index out of range error
|
|
14
|
1107
|
December 4, 2023
|
|
Questions on Non-equilibrium TI Phase with Slurm Scheduler in 'AZtutorial.py' Script
|
|
2
|
184
|
December 4, 2023
|
|
Error using mutate.py with charmm FF
|
|
3
|
165
|
December 1, 2023
|
|
Mutation involving two proteins
|
|
2
|
134
|
November 29, 2023
|
|
Performing Non-equilibrium Alchemical Transformations with Multiple Mutations
|
|
3
|
178
|
November 24, 2023
|
|
Please help me understand these values from the tutorial
|
|
4
|
154
|
November 23, 2023
|
|
Theoretical question about 'one box two systems'
|
|
4
|
142
|
November 22, 2023
|
|
PMX protein mutation tutorial
|
|
6
|
263
|
November 10, 2023
|
|
Different masses of dummy atoms in webserver pmx and standalone pmx
|
|
1
|
207
|
October 31, 2023
|
|
The use of GAFF1 vs GAFF2 with the pmx ff99SB*-ILDN forcefield
|
|
2
|
151
|
October 25, 2023
|
|
Pmx webserver is not running
|
|
1
|
132
|
October 18, 2023
|
|
Help Needed with Protein-Ligand Topology in pmx Tutorial
|
|
4
|
314
|
October 13, 2023
|