|
Apply constraints to desire molecules
|
|
3
|
27
|
March 28, 2025
|
|
Novice to simulate antibody-drug-conjugate -- unnatural residues
|
|
1
|
21
|
March 26, 2025
|
|
cGenFF Ligand topology
|
|
0
|
51
|
March 13, 2025
|
|
How to set the bond constraint of the sidechain in a self-designed peptide
|
|
3
|
25
|
February 18, 2025
|
|
How to perform md simulation on a protein structure which have a ca+ ions
|
|
0
|
29
|
January 23, 2025
|
|
Chloroform as a solvent in Charmm36 force field
|
|
1
|
71
|
January 16, 2025
|
|
Issues with Ligand Topology Creation Using CGENFF and CHARMM-GUI
|
|
2
|
62
|
January 7, 2025
|
|
Atom OXT in residue GLN 336 was not found in rtp entry GLN with 17 atoms while sorting atoms
|
|
3
|
33
|
December 19, 2024
|
|
High Penalty Score in CGENFF topology
|
|
0
|
67
|
December 15, 2024
|
|
Fatal error: number of coordinates in coordinate file does not match topology file
|
|
4
|
1291
|
December 9, 2024
|
|
Applying constraints to different molecules in a same system
|
|
0
|
50
|
November 19, 2024
|
|
Trouble with CGenFF and Ligand Topology in GROMACS
|
|
0
|
160
|
October 19, 2024
|
|
Help with "Inconsistent Residue Types" Error
|
|
1
|
77
|
September 30, 2024
|
|
Error in using cgenff for ligand topology, ligand.str missed bond information
|
|
1
|
30
|
September 27, 2024
|
|
Error in CGenFF: "No valid resonance structure found"
|
|
3
|
31
|
September 26, 2024
|
|
Protein with Ion cofactors
|
|
1
|
27
|
September 6, 2024
|
|
Topology files with packmol
|
|
5
|
509
|
September 4, 2024
|
|
Issues Running GROMACS with Amber Force Field - Seeking Guidance
|
|
1
|
96
|
August 26, 2024
|
|
Problem in generating topology file for nanoporous MoS2 membrane
|
|
0
|
30
|
July 10, 2024
|
|
Topol.top file not generating
|
|
1
|
54
|
July 7, 2024
|
|
.gro no match .top
|
|
3
|
32
|
July 5, 2024
|
|
Build the Topology (adding .prm and .itp)
|
|
3
|
349
|
July 4, 2024
|
|
Problem with chain definition, or missing terminal residues
|
|
1
|
145
|
June 25, 2024
|
|
How to add new residue in the lipids.rtp in charmm27.ff?
|
|
6
|
97
|
June 20, 2024
|
|
How define phosphoaspartate in Charmm36?
|
|
3
|
56
|
June 19, 2024
|
|
MARTINI Parameters for DMG (1,2-Dimyristoyl-rac-glycerol)
|
|
1
|
73
|
June 14, 2024
|
|
Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database
|
|
0
|
114
|
May 6, 2024
|
|
Incorrect relative solvation free energy values using single topology alchemical transformation
|
|
8
|
352
|
May 5, 2024
|
|
Difference between x2top and LigParGen ff generation (dodecane)
|
|
1
|
128
|
April 26, 2024
|
|
Topology versus initial configuration
|
|
2
|
65
|
April 25, 2024
|