AMBER Archive (2004)

Subject: Re: AMBER: NMODE via MM-PBSA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 21 2004 - 06:49:48 CST

ML schrieb:
>
> Hello AMBER team!!!
> Is there any way to do nmode calculations via mm-pbsa stepwise? I mean
> steep desc+conj.grad. mini in sander, then Newt-Raph mini in nmode, then
> normal modes in nmode. What it does now is passing minimization commands
> to sander and urging nmode to do normal mode analysis, not Newt-Rap.

Not without changing the code. Starting points would be the
"create_nmode_input" subroutine, where you would have to add another
input file for nmode to do NR-minimization. Then, another system call to
nmode has to be added to the subroutine "calc_NM" (plus adaptation of
the used filenames). But before you start, please consider that
NR-minimization can be computationally demanding for larger systems (in
fact, this is the reason why your suggested route hasn't been put into
mm_pbsa).

Best regards

Holger

>
> I'd very much appreciate your help.
>
> Sincerely,
>
> 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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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
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
++++++++++++++++++++++++++++++++++++++++++++++++++

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