Re: [AMBER] How by residue decomposition in MMPBSA.py is performed?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 13 Sep 2016 08:28:40 -0400

On Tue, Sep 13, 2016 at 12:53 AM, Irina Ivanova <irinaanatolieva.abv.bg>
wrote:

>
>
>
> Dear Amber users,
>
>
>
>
>
> I want to ask how residue decomposition in MMPBSA.py is perfromed? Are
> terms computed for individual atoms and then all atoms in a residue summed?


​This is the general idea, yes.



> Why with inp=2 (default value) non-polar solvation term is always zero?


I presume because decomposition has not been implemented for per-residue
decomposition with that model.



> What is the practical difference between
> idecomp = 1 and
> idecomp = 2?
>

​This is listed in the manual. If I recall correctly, the 1-4 nonbonded
terms are added either to electrostatic component or the dihedral component
of the energy terms.

HTH,
Jason

-- 
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2016 - 05:30:03 PDT
Custom Search