Re: AMBER: Nmode problem

From: Holger Gohlke <>
Date: Fri, 28 Nov 2003 16:11:49 +0100

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 with nmd_min.out
> possible FAILURE: check nmd_min.out.dif

Here, you need to check the file nmd_min.out.dif in

> ==============================================================
> cd quasih; ./Run.quasih
> Title in input file:
> rdparm transformed trajectory
> diffing 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


Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
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Received on Wed Jan 14 2004 - 15:53:02 PST
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