GROMACS version: 2026.1
GROMACS modification: No
Hi!
I’d like to request some assistance in running gmx_mmpbsa for my system. For context, I’m performing 200 nanosecond runs for a protein-protein complex (receptor and homodimer protein/growth factor). My topology generation is as follows:
gmx pdb2gmx -f protein.pdb -o protein.gro -ignh -water tip3p -ss -merge inter
wherein the pdb contains 3 protein chains (one for the receptor, two for the homodimer ligand) and inter-chain disulfide linkages are present on the homodimer. I’ve recently hit a wall with gmx_mmpbsa, wherein it keeps rejecting my index file.
My index file is as follows
Protein receptor
Homodimer protein ligand (I’ve merged the two monomers)
Since the homodimer contains two individual chains, the numbering repeats, and it gives me this error message:
[WARNING] The complex structure used is inconsistent. The following residues are duplicates:
B:1:ALA:, B:2:PRO:, B:3:MET:, B:4:ALA:, B:5:GLU:, B:6:GLY:, B:7:GLY:, B:8:GLY:, B:9:GLN:…B:121:ARG:, B:1:ALA:, B:2:PRO:, B:3:MET:, B:4:ALA:, B:5:GLU:,
I’m not sure what the workaround for this is, since I have to retain the homodimer as one object, or my mmpbsa calculations would be erroneous (due to inter-chain disulfides and the fact that my protein requires homodimerization for biological activity/binding with protein receptor). I’m trying to calculate the delta G between my protein receptor and homodimer protein, but I can’t proceed due to this error.
Please let me know if more information is needed. Thank you for your time.