AMBER Archive (2004)

Subject: Re: AMBER: Normal modes of protein-ligand

From: bishop (bishop_at_tulane.edu)
Date: Wed Jan 28 2004 - 08:44:20 CST

Can someone comment on
how nmode compares to the covariance of the positional fluctuations as
method of determining entropies?

see: Schlitter, J., Estimation of absolute and relative entropies of
macromolecules using the covariance matrix, in Chemical Physics Letters.
1993. p. 617-21.

Thanks
TOm

Martin Lepsik wrote:

> 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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