AMBER Archive (2003)

Subject: Re: AMBER: nmode, trajectory

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sat Dec 13 2003 - 09:42:39 CST

kbyun_at_wesleyan.edu schrieb:
>
> Hi,
> I'm using nmode for an entropy calucation on my RNA
> molecule. In the run, I have four snapshots. However,
> for snapshots #1 and #3 I do not get the "Total" nor the
> "Vibrational" term. The output file is below. Can
> someone explain why I am getting different outputs for
> each snapshots?

You might want to comment the line "unlink $nmodeout;" in the subroutine
"calc_NM" in mm_pbsa.pl . This will give you the nmode output files from
which the information below is read. See if there is any error message
by nmode.

Best regards

Holger

>
> Thanks,
> Suzie Byun
>
> ----------------------------------------
> NM
> 1
> translational 52.160
> rotational 52.071
> 2
> Total 1966.703
> translational 52.160
> rotational 52.081
> vibrational 1862.462
> 3
> translational 52.160
> rotational 51.968
> 4
> Total 1968.172
> translational 52.160
> rotational 52.056
> vibrational 1863.956
>
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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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