AMBER Archive (2003)

Subject: Re: AMBER: usability of mm_pbsa with ligand - membrane protein - complex

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Aug 28 2003 - 18:01:11 CDT

Frank Boeckler wrote:
>
> Dear Amber users,
>
> is there a possibility to use mm_pbsa with simulations of small organic ligands in a
> membrane protein (lacking an explicit lipid environment) for comparison with the
> experimental binding affinity of the ligands?

The current versions of implicit solvation models that work together
with mm_pbsa (GB in sander or delphi II) don't allow a
more-than-two-media world (i.e. one explicit molecule/complex inside a
continuum region). (The latest version of delphi does though, but I have
no experience with it in the context of mm_pbsa.)

If your ligand binding site is well located within the protein (i.e.
distant from the membrane region), it might be worth trying to use the
current setup.

Best regards

Holger
 
> Thanks in advance for your time.
>
> Kind regards
>
> Frank
>
> ************************************************************
> Frank Boeckler
> Emil Fischer Center
> Department of Medicinal Chemistry
> Friedrich Alexander University Erlangen-Nuernberg
> Schuhstrasse 19
> 91052 Erlangen
> +49-9131-85-24115
> boeckler_at_pharmazie.uni-erlangen.de
> ************************************************************
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla, CA 92037   USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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