|
Grmacs_Drude
|
|
4
|
123
|
December 1, 2023
|
|
Atom P in residue DA 90 was not found in rtp entry DA5 with 30 atoms while sorting atoms
|
|
9
|
61
|
November 20, 2023
|
|
Rtp conversion charmm36
|
|
1
|
341
|
November 17, 2023
|
|
Inserting a modified residue into a protein/DNA chain using pdb2gmx
|
|
7
|
211
|
November 2, 2023
|
|
LINCS WARNING (but with atom duplication)
|
|
2
|
89
|
October 27, 2023
|
|
Force fields
|
|
0
|
86
|
October 21, 2023
|
|
.rtp file generation
|
|
0
|
71
|
October 16, 2023
|
|
Covalent bond between protein and ligand (cobalamin)
|
|
4
|
375
|
October 5, 2023
|
|
Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms while sorting atoms
|
|
3
|
173
|
October 1, 2023
|
|
Error in running pdb2gmx for protein with modified residue
|
|
1
|
146
|
September 30, 2023
|
|
Generating PDB file for custom DNA sequence?
|
|
0
|
94
|
September 27, 2023
|
|
Error: atom C1 not found in buiding block 1MET while combining tdb and rtp
|
|
2
|
282
|
September 26, 2023
|
|
Protein-specific termini
|
|
1
|
109
|
September 15, 2023
|
|
Hybrid molecule topologies for intermolecular distance restraints
|
|
1
|
101
|
August 18, 2023
|
|
Error in conversion of pdb file to gro file
|
|
0
|
116
|
August 13, 2023
|
|
Md simulation
|
|
1
|
94
|
August 9, 2023
|
|
Pdb2gmx does not make disulfide bond between peptide chains
|
|
5
|
433
|
July 31, 2023
|
|
Fatal Error "Invalid dihedral type 180
|
|
3
|
363
|
July 8, 2023
|
|
GROMOS54a7 ff leads to missing parameters in topology after S-S-bonds between Cys residues were app
|
|
1
|
202
|
July 5, 2023
|
|
All lipids defined as part of one molecule in topology
|
|
10
|
267
|
July 4, 2023
|
|
Interactive protonation assignment for IgG4 with the charmm36 force field
|
|
3
|
177
|
July 3, 2023
|
|
Missing parameters in cyclic peptide with Gromos FF
|
|
0
|
128
|
July 3, 2023
|
|
Running pdb2gmx on large water/membrane system
|
|
0
|
197
|
June 22, 2023
|
|
Combine LigParGen and Packmol to make Gromacs input
|
|
1
|
609
|
June 13, 2023
|
|
Pdb2gmx Error - molecule in input file was mapped to entry in topology, but atom not found
|
|
0
|
113
|
June 6, 2023
|
|
Protonation/disulfide issues with pdb2gmx?
|
|
1
|
135
|
May 30, 2023
|
|
Error while running writing the topology
|
|
0
|
146
|
May 18, 2023
|
|
Protonation states using -inter
|
|
1
|
136
|
May 11, 2023
|
|
Hydrogen mass repartitioning with 2fs steps
|
|
0
|
149
|
May 4, 2023
|
|
Gmx make_ndx using em.tpr. Fatal error: No v in input file
|
|
9
|
512
|
April 28, 2023
|