AMBER: Normal modes of protein-ligand

From: Martin Lepsik <>
Date: Wed, 28 Jan 2004 13:43:12 +0000

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?

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

3) Or manually taking snapshots out of trajectory, minimize with
dist-dep. diel 4r: sander steep. desc+conj.grad to converg 10E-4.Select
active site only, minimize nmode Newt-Raph to converg 10E-4 then nmode
vibration analysis. At what stage is it best to start using the active
site only? Is it useful to apply some constraints in the Newt-Raph.

Looking forward to your replies. Thanks.

Best regards,

  Martin Lepsik

Martin Lepsik
Dept. of Molecular Modeling
Institute of Organic Chemistry & Biochemistry
Czech Academy of Sciences
phone: +420-220 183 540
fax:+420-220 183 292

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Received on Wed Jan 28 2004 - 12:53:17 PST
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