> On Mar 4, 2015, at 12:04 AM, danieldefoe <daniel.defoe.cadd.outlook.com> wrote:
>
> Dear all, Could we use Amber to calculate interaction energy between any two residues of one protein? I tried with this command: MMPBSA -i filename.in -d filename.dat -do filename2.dat -sp complex_solvated.prmtop -cp complex.prmtop -x filename.mdcrd Is this correct?
You can get something resembling the interaction energy between two residues using MM/PBSA decomposition analysis. The command-line you used looks OK, except you need to use MMPBSA.py instead of MMPBSA.
But your input file matters as much as your command-line. I would suggest consulting the Amber 14 manual with regards to the various options in MMPBSA.py.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 05:00:03 PST
