Binding free energy calculation of a protein-protein complex

[Aditya Padhi]

Dear g_mmpbsa users,

I have a protein-protein complex in a single PDB file (let's say protein-A and protein-B in one PDB file) and I want to calculate the binding free energy between each of the residues between protein-A and protein-B, for which I have already carried out simulation in Gromacs.

I have all the required input files. When I execute "g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../pbsa.mdp -pdie 2 -pbsa -decomp" command, it asks for selecting the 2 groups from index file. The problem is unlike protein-ligand, I have 2 proteins instead as I said earlier. So, how can I select the 2 groups as I have the 2 proteins in the same single PDB file. Although I tried to make the index file by choosing only the proteins when asked, at the end the g_mmpbsa doesn't write the energy values to energy_MM.xvg -p polar.xvg -a apolar.xvg (or sasa.xvg) files.

Can anyone please suggest, where I have to make the changes so that I can separately choose the 2 proteins for making the index file and can calculate the binding free energies.

Thank you so much,
Addy

[g_mmpbsa Mailing List]

You have to make two separate index groups for both sub-units and then select these two index groups with g_mmpbsa command.