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Protonation/disulfide issues with pdb2gmx?
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1
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20
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May 30, 2023
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Error while running writing the topology
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0
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37
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May 18, 2023
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Protonation states using -inter
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1
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34
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May 11, 2023
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Pdb2gmx does not make disulfide bond between peptide chains
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4
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89
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May 4, 2023
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Hydrogen mass repartitioning with 2fs steps
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0
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24
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May 4, 2023
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Gmx make_ndx using em.tpr. Fatal error: No v in input file
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9
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161
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April 28, 2023
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Combine some topologies
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0
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28
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April 27, 2023
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Unknown cmap torsion between atoms near modified residue
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0
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35
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April 20, 2023
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Is it possible to define improper dihedral angles for sidechain-backbone crosslinks
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0
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37
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April 12, 2023
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Capping residue ACE not recognised from the rtp file
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14
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2042
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April 12, 2023
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Generate topolgy file using pdb and itp files
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2
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197
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March 16, 2023
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Fatal errors in .rtp file
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2
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67
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March 16, 2023
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Pdb2gmx does not recognize disulfides accurately
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2
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77
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March 15, 2023
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Fatal errors
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0
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64
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March 1, 2023
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Error message
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2
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60
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February 26, 2023
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Error in pdb2gmx command
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2
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114
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February 25, 2023
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PDB2GMX for Modified DNA_CHAIN
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4
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52
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February 17, 2023
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Can't create topology for small molecule using pdb2gmx/x2top
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1
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139
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February 10, 2023
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Errors in generating topology for RNA with unnatural residues
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3
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666
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February 8, 2023
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Mdrun Instability with deprotonated ARG topology with CHARMM36
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0
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57
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January 12, 2023
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LINCS algorithm warning dueing NVT run
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0
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55
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January 5, 2023
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Atom C1 not found in building block (pdb2gmx fatal error)
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3
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259
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November 21, 2022
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Strage behaviour - pdb2gmx
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2
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260
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October 19, 2022
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Covalent bond between protein and ligand (cobalamin)
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3
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127
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October 11, 2022
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Introducing New atom to the Gromacs forcefield
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2
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120
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September 28, 2022
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Problem in generating topology file of a polymer
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9
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295
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September 21, 2022
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A shift in molecules between topol.top and solv.gro
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1
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92
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September 18, 2022
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Warnings in Gromacs
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6
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163
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September 7, 2022
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Why huge amount of SOL added during gmx genion in some cases?
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5
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176
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September 3, 2022
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Little to no movement or change in protein structure after 50ns MD
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2
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137
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September 2, 2022
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