Running Protein simulation with multiple ligands

GROMACS version: 2018

Hello everyone,
I am new to GROMACS and trying to run a protein simulation with chromophores FAD and DLZ and DNA as ligands using Amber ff99sb force field. While running the simulation how should I generate the index files for the chromophores? Should I generate three different index files each for FAD DLZ and DNA and then club it as one? In that case how should I do that? or is there any other way for indexing multiple ligands. Thank you very much for your help.

to generate an index file you can use the tool gmx make_ndx gmx make_ndx — GROMACS 2022.2 documentation or gmx select gmx select — GROMACS 2022.2 documentation. An index file can contain several groups. You can define a group for each chromophore if you want.

Thank you very much for your help. It worked. Could help me regarding restraining the DNA ligand, in the same system? Thank you.

do you mean how to position-restrain the DNA? Or do you refer to other type of restraints (Restraints — GROMACS 2022.2 documentation)?


Yes I mean the position restraint of DNA in a Protein-DNA simulation.

FIrst you need a posre.itp type of file in the working directory and this file has to be correctly included in the topology file. To do that you can use gmx genrestr — GROMACS 2022.2 documentation. The tool generate the file you needs and include them in the topology.
If you have use gmx pdb2gmx to create the topology of the whole system, a position restrain file for DNA (e.i posre.itp type of file) has been already created and include in the proper place in the topology files.

Then you tell the program to use posre file, and you can do it in the in mdp file using the option define

defines to pass to the preprocessor, default is no defines. You can use any defines to control options in your customized topology files. Options that act on existing top file mechanisms include

-DPOSRES will trigger the inclusion of posre.itp into your topology, used for implementing position restraints.

For example at the end of the dna.itp file you read something like this
#ifdef POSRESdna
#include “posre_DNA.itp”

Then define = -DPOSRESdna in the mdp file. This will activate the position restrain only on the DNA, only if POSRESdna is only defined in the dna.itp.