On Wed, May 22, 2013 at 8:34 AM, <dilrajl.bii.a-star.edu.sg> wrote:
> Dear Amber Users,
> I have done simulation of a protein-peptide complex.
> I now want to perform the pairwise decomposition analysis using
> mmpbsa.py.
>
> My input script for the purpose is as follows:
>
> sample input file for MM-GBSA calculation and DECOMPOSITION
> &general
> startframe=1, endframe=10, interval=5,
> verbose=2, keep_files=2,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &decomp
> idecomp=3,
> dec_verbose=0,
> csv_format=0,
> /
>
> This gives the pairs-wise decomposition of every residue-pair within
> the protein, peptide and between the protein-peptide.
>
> I want to restrict the calculation to only say the residues from the
> peptide and protein or say between specific pairs of residue between
> the protein-peptide.
>
> I believe this will reduce the computational cost and also the printed
> file size.
>
> Can someone please give me suggestion on how to do this?
>
Look at the print_res variable. This will print out the energy between
every pair of residues in print_res. There is currently no way to provide
2 lists so that only interactions between two residues present in each of
the lists will be printed.
If that was unclear, here's an example. If you want the interaction between
residues 10 and 20, then set "print_res = 10, 20". If you want the
interactions between residues 10 and 20 and residues 10 and 30, then you
will need to set "print_res = 10, 20, 30", but this will also print out the
20-30 interaction, since both are in the list (there is no way to avoid
this).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 22 2013 - 06:00:06 PDT
