Hi Md. Sahadot Hossen ,

If two proteins are separate, you can combine them in one file and then do it like a simulation of protein in water, because the force field parameters for protein and DNA molecules are available in GROMACS, and there is no need to generate a manual topology. For example, if the names of the proteins are receptor and ligand:

1) gmx editconf -f receptor.pdb -o receptor.gro -box X Y Z -c

(You have to define the coordinates of X, Y, and Z for the box size)

2) gmx insert-molecules -f receptor.gro -ci ligand.pdb -nmol 1 -o system.pdb

Then use the system.pdb file for the gmx pdb2gmx command.

Not sure if you have done protein-protein docking to identify the potential binding regions between your proteins. If so, you can use GROMCAS lysozyme tutorial unless your protein has modified residues such a residue with post-translational modification. A quick and simple way to generate topology is CHARMM-GUI.

Hello Mr. Hamed Zahraee,

I have run the simulation today, and it is okay. I prepared the protein topology using charmm 36 force field and then ligand topology.

Adding the lig.gro file in _processed.gro file and made complex.gro file.

You showed me another way, I will try it.

Thanks for your comment.

I have a docked protein-protein complex (lets say Chain A: 1 to 350 and ChainB: 351 to 570).

How do I make an index file to create rmsd, rmsf graph

Dear Md. Mashiur Rahaman,

1) To create an index file for RMSD calculation, type the following commands and press enter:

1> gmx make_ndx -f md.gro -o chain_CA.ndx

2> splitch 3

3> q

4> gmx rms -f md.xtc -s md.tpr -n chain_CA.ndx -o rmsd_chain_A.xvg

Select chain A in index numbers

Select chain A in index numbers

5> gmx rms -f md.xtc -s md.tpr -n chain_CA.ndx -o rmsd_chain_B.xvg

Select chain B in index numbers

Select chain B in index numbers

2) To create an index file for RMSD calculation, type the following commands and press enter:

1> gmx make_ndx -f md.gro -o chain.ndx

2> splitch 1

3> q

4> gmx rmsf -f md.xtc -s md.tpr -n chain.ndx -o rmsf_chainA.xvg

Select chain A in index numbers

5> gmx rmsf -f md.xtc -s md.tpr -n chain.ndx -o rmsf_chainB.xvg

Select chain B in index numbers

If you need help, upload the .gro file of the simulation output, so I can guide you.

Generate the entire topology with pdb2gmx. You have two proteins, nothing more. The second protein is not a “ligand” in the typical sense, which refers to some arbitrary species that is not covered by the force field. Never generate a protein topology with a general force field.