AMBER Archive (2003)

Subject: Re: AMBER: Nmode problem

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Fri Nov 28 2003 - 09:11:49 CST

Wu Yingliang schrieb:
>
> Dear Amber users,
>
> I am using amber7 in Red Hat Linux 9.0. There are something wrong with Nmode. When I test Nmode in
> $AMBERHOME/test directory, some possible failures appear. At first, I did not care about it. However, examples
> of "Nmode" calculation for estimating entropies by MM-PBSA can not be correctly run.

>From the information you provide it is almost impossible to say what
went wrong. "... cannot be correctly run" - does it mean it doesn't run
at all or does it mean it yields "wrong" results but terminates
correctly? What does the ouput file say at the end?

...
> cd newton_raph; ./Run.newton_raph
> diffing nmd_min.out.save with nmd_min.out
> possible FAILURE: check nmd_min.out.dif

Here, you need to check the file nmd_min.out.dif in
$AMBERHOME/test/newton_raph.

> ==============================================================
> cd quasih; ./Run.quasih
> Title in input file:
> rdparm transformed trajectory
>
> diffing quasih.out.save with quasih.out
> possible FAILURE: check quasih.out.dif

Same as above with quasih.out.dif. Note that quasih and nmode are
different programs.

> Looking forward to help! Thanks a lot in advance!

Looking forward to more specific information - best regards

Holger 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
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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