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Difference between x2top and LigParGen ff generation (dodecane)
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1
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21
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April 26, 2024
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Problem with pdb2gmx as it says there is no resdiue type XXX
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6
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52
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April 26, 2024
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How to add C2O or Cu2O in residuetypes.dat
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8
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189
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April 24, 2024
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Water molecules for ion coordination in simulation
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0
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26
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April 23, 2024
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Bond between protein and ligand
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4
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57
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April 19, 2024
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What are your thoughts on my MD step at preprocessing?
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1
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37
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April 16, 2024
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About the water molecules
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14
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87
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April 15, 2024
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C-terminus protonation using PDB2GMX
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2
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86
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April 4, 2024
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Gmx pdb2gmx error
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3
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52
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April 2, 2024
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Pdb2gmx long bond warning
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4
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73
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March 21, 2024
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Creating topology for chimeric DNA/RNA strand
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0
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75
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March 19, 2024
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Error while sorting atoms
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2
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65
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March 13, 2024
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How to generate topology for a single aminoacid residue?
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0
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66
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March 12, 2024
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Topology files with packmol
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4
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89
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March 6, 2024
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Problem with acetylated and amidated termini in pdb2gmx command
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1
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402
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March 6, 2024
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Molecular dynamic simulation of alkaloids
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0
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83
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March 2, 2024
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PACKMOL and gmx2pdb
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0
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106
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February 20, 2024
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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18
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777
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February 17, 2024
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Overiding bonded parameters from ffbonded.itp by explicitly specifying in residue.rtp
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0
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93
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February 16, 2024
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Urgent: Queries regarding the gromacs file synthesis for DNA-lipid systems
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5
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153
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February 15, 2024
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Atom not recognized, but clearly is in the pdb [pdb2gmx using Charmm36]
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3
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155
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February 14, 2024
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Fatal error: Atom HO2' in residue A 21 was not found in rtp entry ADE with 31 atoms while sorting
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1
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126
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February 6, 2024
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Fatal error: number of coordinates in coordinate file does not match topology file
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2
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325
|
February 3, 2024
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Fatal Error atom C2 not found in building block 465MET while combining tdb and rtp
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1
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116
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January 28, 2024
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How can I generate a toplogy from a pdb file with non-standard residues?
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1
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126
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January 25, 2024
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Loading a Ecoli Ribosome structure in Gromacs 6i0y/4v7u
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2
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96
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January 24, 2024
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Pdb2gmx does not recognize disulfides accurately
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3
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399
|
January 5, 2024
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Protonation/disulfide issues with pdb2gmx?
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2
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320
|
January 5, 2024
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Fatal error while running gromacs. Atom N not found in building block 1DG while combining tdb &rtp
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1
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144
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January 3, 2024
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How to include a itp file to gromacs forcefiled
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5
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333
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January 2, 2024
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