Building a pdb2gmx file with a covalently bound ligand to DNA

User discussions
1

GROMACS version: 2023.4
GROMACS modification: No
Here post your question

Hello everyone,
I am working on DNA with two covalently bound modified cholesterol chains. I am unable to make the pdb2gmx file. I have generated the itp and prm file using CGENFF python script. But, I am unable to proceed further as the rtp file for the modified cholesterol and the parameters required are not present. Can anybody tell me the procedure for generating the pdb2gmx file with the covalently bound ligand.

Thank you in advance

2

There are tools to introduce bonds between residues with existing topologies, so depending on how reliable your CGenFF parameters are, and what is the size/compatibility of the residue you decided to parametrize, it might help in this particular case. Alternatively (and perhaps easier to do in practice), there’s a function that converts an .itp to an .rtp - remember to check if impropers are correctly assigned though, and make/edit a local copy of residuetypes.dat before running pdb2gmx.