AMBER Archive (2004)

Subject: Re: AMBER: question about mmpbsa

From: xhu1_at_memphis.edu
Date: Wed Dec 08 2004 - 16:23:27 CST

Dear Fabien,

Thank you so much for your reply. You are right. It's very helpful.

All the best

Shawn
 
----- Original Message -----
From: cailliez <Fabien.Cailliez_at_ibpc.fr>
Date: Wednesday, December 8, 2004 12:23 pm
Subject: Re: AMBER: question about mmpbsa

> Dear Shawn,
>
> When you set INDI in the input script, you only change the
> internal
> dielectric
> for PB solvation energies calculation with delphi.
> But all the other energies are calculated in sander with an
> internal
> dielectric of 1. That is
> why ELE and GB energies do not change and they are calculated with
> an
> internal dielectric
> value of 1 (if I understood correctly the mm_pbsa scripts).
> In order to change these values you have to change the mm_pbsa.pl
> script
> to modify the
> sander input file created during the MM/GB calculations,
> introducing the
> intdiel variable.
> Here is the diffing report between the initial script and the one
> that I
> changed to introduce an
> internal dielectric of 2 :
> 804c804
> < print OUT " idecomp= ${idecomp}, intdiel = 2,\n";
> ---
> > print OUT " idecomp= ${idecomp},\n";
>
> Good luck,
> Fabien
>
> --
> __________________________________________________________________
> Fabien Cailliez Tel : 01 58 41 51 63
                                
> Laboratoire de Biochimie Th¨¦orique e-mail : cailliez_at_ibpc.fr
> IBPC 13, rue Pierre et Marie Curie
> 75005 Paris
> __________________________________________________________________
>
>
>
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