AMBER Archive (2004)

Subject: Re: AMBER: question about mmpbsa

From: cailliez (
Date: Wed Dec 08 2004 - 12:23:01 CST

Dear Shawn,

When you set INDI in the input script, you only change the internal
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 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 :
< 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 Théorique e-mail : IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to