On Wed, Sep 19, 2012 at 4:44 PM, Kasam, Vinod <vkasam.coh.org> wrote:
> Dear Amber users,
>
> I was able to use MMPBSA.py on a trajectory obtained from MD simulation,
> However, can some body tell me how to run MMPBSA.py on a single protein
> (not generated from a MD simulation).
>
> How does the mmpbsa.in (input file) and syntax MMPBSA.py -O .... look
> like,
>
You need to specify the structure using the '-y' flag of MMPBSA.py (you
still need the relevant topology files, though). Any file format that
cpptraj recognizes (PDB, mol2, mdcrd, netcdf, dcd, etc.) will work for
MMPBSA.py.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 19 2012 - 14:30:03 PDT
