AMBER Archive (2004)

Subject: AMBER: MM-PBSA: molecular charges and active site water

From: Anselm Horn (Anselm.Horn_at_biochem.uni-erlangen.de)
Date: Thu Feb 12 2004 - 09:23:05 CST

Dear all,

I intend to use the MM-PBSA method to calculate the binding energy of a
ligand-receptor system. As I am new user this method, I have two questions:

1,
Is the total charge of the system of crucial importance for MM-PBSA
calculations, i.e. should both ligand and receptor be electrically neutral? Is
there a problem, if the ligand and receptor have the same charge but opposite
sign? However, counterions, when added to the complex, are to be excluded from
the ligand/receptor definition in mm_pbsa.pl in any case.

2,
My system contains some active site water molecules that are hidden from the
rest of the solvent by the ligand/receptor environment. How do I include those
in the MM-PBSA calculation? Is it feasable to make them belong to the receptor
or do I have to treat the other case as well, where they belong to the ligand?

(I apologize for possible reposting those questions, but I couldn't find an
answer in the archives.)

Many thanks in advance for any hints and answers,

Anselm 

-- 
Abteilung f. Bioinformatik
Institut f. Biochemie
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Fahrstrasse 17
91054 Erlangen
Tel.: +49-9131-85-24682
Germany

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