It sounds like your complex, receptor, and ligand atom number definitions
are incorrect in your input file.
-Bill
On Mon, Aug 22, 2011 at 5:35 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am trying to use the mm_pbsa decomposition module for residue pairwise
> energy
> calculation. However, when I extract the snapshots for mm_pbsa using
> standard
> extraction script, the resulting crd files (input to decomposition) seem to
> have
> some residues broken up when converted to pdb. When I convert the same
> trajectory snapshots into pdb using ptraj, nothing goes wrong with the
> structure.
>
> Please help me with this problem.
>
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee
>
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Aug 23 2011 - 11:00:04 PDT
