Re: AMBER: Normal modes of protein-ligand

From: Holger Gohlke <>
Date: Wed, 28 Jan 2004 20:32:49 +0100

Martin Lepsik schrieb:
> Dear AMBER team,
> I am trying to estimate TdS of a 3000-atom protein using mm-pbsa and
> nmode. My question is, what methodology is recommended:
> 1) Are some 3 snapshots doable in reasonable time on Opterons with 8GB
> memory or Altix Itanium Medison with 32GB?

If I remember right, minimizing a ~3500 atom protein on a single R14000
cpu to a rms gradient < 10^-4 kcal/(mol A) took about 6-7 hours using
the conj. grad. method in sander. Calculating vibrational entropies on
an Itanium2 (?) using a 64 bit version of nmode needed about 2GB of
memory and took about 45 min. So I'd say that your suggestion above is

> 2) Using nmode, can I choose some parts (active site) for nmode? What is
> the format for BELLY groups in mm_pbsa?

Currently, no belly groups can be specified via the script.

Best regards


Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
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Received on Wed Jan 28 2004 - 19:53:01 PST
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