|
How to add terminal caps in AMBER with GROMACS
|
|
1
|
11
|
December 3, 2025
|
|
How to include bound calcium in amylase structure
|
|
4
|
23
|
November 21, 2025
|
|
Error Query Regarding pdb2gmx Generating TOP Files Containing DNA Fragments
|
|
1
|
25
|
November 15, 2025
|
|
Pdb2gmx not recognizing water block
|
|
1
|
30
|
November 11, 2025
|
|
How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
|
|
9
|
144
|
October 26, 2025
|
|
Topology files with packmol
|
|
6
|
668
|
October 20, 2025
|
|
GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
|
|
2
|
55
|
October 14, 2025
|
|
what should do with zink-protein.pdf to get topology file?
|
|
5
|
46
|
October 7, 2025
|
|
Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
|
|
2
|
42
|
October 5, 2025
|
|
How to deal with protonation state in GROMACS? (encountering fatal error)
|
|
4
|
71
|
September 29, 2025
|
|
CNT creation having more than 999 atoms
|
|
3
|
40
|
September 19, 2025
|
|
The amino acids reported as errors by pdb2gmx do not correspond to the amino acids in the structure
|
|
1
|
13
|
September 19, 2025
|
|
How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
|
|
0
|
28
|
August 28, 2025
|
|
Question about Changing DNA residues to Protein in residuetypes.dat for covalent bond
|
|
1
|
20
|
August 4, 2025
|
|
Why Does GROMACS Rename a DG Terminus to DG5 Without Manual Patching?
|
|
0
|
19
|
July 22, 2025
|
|
Homocysteine covalently bonded with a protein MD simulation how to perform
|
|
0
|
37
|
July 21, 2025
|
|
Pdb2gmx: -ter option doesn't work
|
|
1
|
63
|
July 16, 2025
|
|
How to create restrained file for sol
|
|
0
|
21
|
July 15, 2025
|
|
Potential bug in pdb2gmx
|
|
1
|
37
|
May 20, 2025
|
|
System has non-zero total charge: -1.000000
|
|
1
|
32
|
May 19, 2025
|
|
Fatal error: Residue 175 named GLU of a molecule in the input file was mapped to an entry in the top
|
|
0
|
27
|
May 18, 2025
|
|
Atom C1 not found in building block 1MET while combining tbp and trp
|
|
0
|
67
|
May 18, 2025
|
|
How to simulate d-amino acids
|
|
10
|
381
|
March 8, 2025
|
|
Issue with pdb2gmx with MT-COX2 gene
|
|
0
|
29
|
February 27, 2025
|
|
Inconsistency in user input: Could not find force field 'martini3.ff' in current directory, install
|
|
0
|
76
|
February 24, 2025
|
|
How to set the bond constraint of the sidechain in a self-designed peptide
|
|
3
|
28
|
February 18, 2025
|
|
Adding a new residue covalently linked to multiple cysteines
|
|
0
|
37
|
February 6, 2025
|
|
Pdb2gmx not able to form bonds in an unusual ligand
|
|
5
|
99
|
January 30, 2025
|
|
How to perform md simulation on a protein structure which have a ca+ ions
|
|
0
|
61
|
January 23, 2025
|
|
Topology of an ACE-linked cyclic peptide with a free C-ter
|
|
0
|
54
|
January 23, 2025
|