Adding .prm and .rtf file in residue topology for new molecule in charm36force field

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1

GROMACS version:
GROMACS modification: Yes/No
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I want to know that how to add new revised force field for a new molecule, while I am using charmm36 July 2021 force field. Where to add .rtf and .prm files of new molecule. @jalemkul.
Because I am getting error xxxxx is not found in residue topology. When I added these files to my Charmm36jul2021 force field folder

2

You need to make sure the topol.top file is accessing the topology of the new molecule. This tutorial takes you through the basics of adding a custom topology for a new molecule to your forcefield, the steps should work for your case

3

You are right, but I am getting this fatal error at this command “gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce” the topol.top not generated still then how to add this.

4

pdb2gmx doesn’t work if the topology isn’t already part of the forcefield. If your simulation doesn’t have a molecule that the topology has defined, then you either need to manually create the topol.top file yourself, or do pdb2gmx on a molecule that you know the forcefield has defined, then remove that molecule from the topol.top file and edit the file to fit the system you want to simulate

5

Thank you for information will do it.