Dear AMBER users,
I am trying to run MMGBSA analysis using mm_pbsa.pl for a heme-bound
protein monomer with its ligand. My issue is that the receptor atoms are
not numbered continuously, as one of the *monomer protein residue atoms is
from 1–6160*, and the second segment, i.e., *cofactor heme group residue
atoms, is from 12321–12393*. The ligand is defined from atoms no.
*12467–12507*.
In the input file, I tried to specify multiple receptor groups using
RSTART/RSTOP (mentioning two groups of receptor with RSTART1, RSTOP1,
RSTART2 and RSTOP2), but mm_pbsa.pl gives the error: "*Something wrong
with RSTART definitions*."
I would like to know the correct way to define a receptor while extracting
coordinates while doing MMGBSA analysis when the receptor atoms are split
into two or more non-contiguous groups. I would be grateful if you could
guide me on this.
Thanks and regards,
Pranita Patil
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Received on Thu Aug 28 2025 - 10:30:02 PDT
