Generate topolgy file using pdb and itp files

User discussions
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GROMACS version: 2022.4
GROMACS modification: No

Hello gromacs users, I am fairly new to gromacs and molecular dynamics. I want to simulate thiols for starters for some applications and I want to generate the topology file for thiol. I found the PDB and ITP files for sulfanyl from ATB and I tried to use ‘pdb2gmx’. I have read up on the documentation but I can’t get it to work. I am stuck on how to modify a forcefield or how to simply create a new one for the molecule. Any help on how to generate the topology would be greatly appreciated. Thanks

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Hi,
I am not familiar with ATB. I do not know exactly how the generated itp file looks like. It could be that you do not need the pre-processing tool gmx pdb2gmx.
In general to know more on topology files in GROMACS this manual page https://manual.gromacs.org/current/reference-manual/topologies/topologies.html can be useful
Note that topology file in GROMACS are hierarchical this table on topology format can be useful https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
Maybe those page can help to understand file you got from ATB.

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Thanks alevilla! I have progressed somewhat on the issue.