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?
Thank you,
Dilraj.
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Received on Wed May 22 2013 - 06:00:04 PDT
