Hi
Is there a reason you are using the perl version for mmgbsa?
The python version is more updated and easy to use. The atom masks for
receptor, even if, not continuous, can be handled well.
On Thursday, 28 August 2025, Patil Pranita Uttamrao via AMBER <
amber.ambermd.org> wrote:
> 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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Best Regards
Elvis
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Received on Thu Aug 28 2025 - 11:00:03 PDT
