|
X2top not generating listed interactions correctly
|
|
1
|
48
|
July 23, 2026
|
|
`opc.gro` available on GitHub
|
|
1
|
159
|
April 13, 2026
|
|
How to build Ligand topology
|
|
2
|
170
|
February 4, 2026
|
|
Fatal error: number of coordinates in coordinate file does not match topology file
|
|
7
|
1953
|
January 7, 2026
|
|
Topology files with packmol
|
|
6
|
900
|
October 20, 2025
|
|
Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
|
|
2
|
110
|
October 5, 2025
|
|
x2top for MINFF
|
|
0
|
94
|
October 2, 2025
|
|
How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
|
|
0
|
63
|
August 28, 2025
|
|
Modifying topol.top with each step of peptide insertion over membrane from CHARMM-GUI
|
|
2
|
116
|
August 2, 2025
|
|
Does bond order in MOL2 file affect rtp generation and pdb2gmx?
|
|
2
|
78
|
June 5, 2025
|
|
Confusion over RB and Fourier Dihedrals
|
|
0
|
58
|
May 29, 2025
|
|
Apply constraints to desire molecules
|
|
3
|
102
|
March 28, 2025
|
|
Novice to simulate antibody-drug-conjugate -- unnatural residues
|
|
1
|
58
|
March 26, 2025
|
|
cGenFF Ligand topology
|
|
0
|
197
|
March 13, 2025
|
|
How to set the bond constraint of the sidechain in a self-designed peptide
|
|
3
|
65
|
February 18, 2025
|
|
How to perform md simulation on a protein structure which have a ca+ ions
|
|
0
|
114
|
January 23, 2025
|
|
Chloroform as a solvent in Charmm36 force field
|
|
1
|
234
|
January 16, 2025
|
|
Issues with Ligand Topology Creation Using CGENFF and CHARMM-GUI
|
|
2
|
535
|
January 7, 2025
|
|
Atom OXT in residue GLN 336 was not found in rtp entry GLN with 17 atoms while sorting atoms
|
|
3
|
135
|
December 19, 2024
|
|
High Penalty Score in CGENFF topology
|
|
0
|
169
|
December 15, 2024
|
|
Applying constraints to different molecules in a same system
|
|
0
|
98
|
November 19, 2024
|
|
Trouble with CGenFF and Ligand Topology in GROMACS
|
|
0
|
296
|
October 19, 2024
|
|
Help with "Inconsistent Residue Types" Error
|
|
1
|
202
|
September 30, 2024
|
|
Error in using cgenff for ligand topology, ligand.str missed bond information
|
|
1
|
86
|
September 27, 2024
|
|
Error in CGenFF: "No valid resonance structure found"
|
|
3
|
108
|
September 26, 2024
|
|
Protein with Ion cofactors
|
|
1
|
75
|
September 6, 2024
|
|
Issues Running GROMACS with Amber Force Field - Seeking Guidance
|
|
1
|
220
|
August 26, 2024
|
|
Problem in generating topology file for nanoporous MoS2 membrane
|
|
0
|
74
|
July 10, 2024
|
|
Topol.top file not generating
|
|
1
|
103
|
July 7, 2024
|
|
.gro no match .top
|
|
3
|
120
|
July 5, 2024
|