AMBER Archive (2005)

Subject: Re: AMBER: nmode in mmpbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue May 17 2005 - 01:44:17 CDT

Am Dienstag, 17. Mai 2005 01:36 schrieb Joseph Fernandez:
> I notice that the .restrt files that are generated
> from nmode during a mmpbsa run cannot be read by
> ptraj.

I think you mean the .restrt file that is generated by a sander minimization
prior to calling nmode here.

> When I open one of these files with vim, the
> file appears to be binary, rather than text. I am
> wondering if there is a way to extract these files and
> create PDB files for visualization.

If you set "ntxo = 1" in the function create_nmode_input in the file
mm_pbsa_createinput.pm, you will get a formatted .restrt file. To use this
for further nmode calculations, you also need to set "ntx = 1" in the same
function.
The reason why a binary .restrt file is output is that using the formatted
version instead reduces the precision in the atomic coordinates, which will
have an influence on the gradient.

Best regards

Holger

>
> Any assistance would be appreciated.
>
> Joe
>
>
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

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

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
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