Dear AMBER community,
I have a (homo)tetrameric protein bound by 4 identical ligands in 4
analogous binding sites. I'd like to calculate binding energies for each of
the 4 identical ligands (identical residue name LIG, atom names, etc.).
In the trajectory/structure file, my protein residues have residue numbers
1-1000, and ligands 1001-1004.
According to my _MMPBSA_receptor.pdb and _MMPBSA_ligand.pdb files,
MMPBSA.py seems to determine the ligand based on the topology file, which I
think does not contain information on residue number. In my case, it
treated the first occurrence of LIG, residue number 1001, as the ligand
regardless of my "ligand_mask" setting to residue number 1002 or 1004 in
the input file.
I also got a CalcError with "mmpbsa_py_energy" failed with prmtop
complex.prmtop!".
What would be a good strategy to force MMPBSA.py to treat residue number
1004, 1003, or 1002 as the ligand with the rest 1003 residues as the
receptor?
Thanks,
Yun
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Received on Wed Sep 06 2023 - 19:00:02 PDT
