AMBER Archive (2004)

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

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 28 2004 - 13:38:57 CST

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

Applying a quasiharmonic analysis to trajectories of proteins of ~75,
~170, and ~240 residues, we encountered problems in getting converged
estimates of the vibrational entropies within 10ns of simulation time
(see J. Comput. Chem. 2004, 25, 238-250).

Best regards

Holger

> 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
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> --
> http://dna.cbr.tulane.edu
>
> Center for Bioenvironmental Research
> Tulane and Xavier Universities
> 1430 Tulane Avenue SL-3
> New Orleans, LA 70112
> Phone: 504-988-6203 Fax: 504-585-6428
> bishop_at_tulane.edu
> -----------------------------------------
> Alternate Contact:
> Center for Computational Sciences
> Voice: (504) 862-8391
> -----------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu