AMBER Archive (2004)

Subject: AMBER: Normal modes of protein-ligand

From: Martin Lepsik (lepsik_at_minea.uochb.cas.cz)
Date: Wed Jan 28 2004 - 07:43:12 CST

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.
minimization?

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
e-mail:lepsik_at_uochb.cas.cz

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