AMBER Archive (2003)

Subject: Re: AMBER: Nmode Problem

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Nov 13 2003 - 13:13:45 CST

Yuqin Cai wrote:
>
> Dear Amber Users,
>
> I run into a problem when I am trying to analysis the entropy using
> Nmode in Amber7.0. The input file is much the same with the example
> from amber.
>
> Do anybody have any suggestions?
>
> %temp/amber7_bug/exe/mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
>
> Here is the error message,
>
> Use ofuninitialized value at
> /local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259. Use of
> uninitialized value
> at/local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259. Use
> of
> uninitialized value at
> /local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm
> line 1259.Use of uninitialized value at
> /local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259.
>
> Here is mm_pbsa.log file,
>
> =>> Init data
> Presuming executables of amber suite to be in
> /local/etc/amber7/exe
> =>> Reading input parameters
> Found PREFIX => dna
> Found PATH => ./selected/
> Found COMPLEX => 0
> Found RECEPTOR => 1
> Found LIGAND => 0
> Found RECPT => ./mtgtnowat.top
> Found GC => 0
> Found AS => 0
> Found DC => 0
> Found MM => 0
> Found GB => 0
> Found PB => 0
> Found MS => 0
> Found NM => 1
> Found DIELC => 4
> Found MAXCYC => 5000
> Found DRMS => 0.1
> Found DELPHI =>
> /home/caiy/rotation_project/new/TGT/minustgt/delphi
> =>> Checking sanity
> Checking GENERAL
> Checking NM =>> Creating input
> Nmode input =>> Calculating energy / entropy contributions
> Calc contrib for ./selected/dna_rec.crd.1
> Minimize structure
> Calc entropy =>> Doing statistics =>> Values of global
> variables
> TEMP = 300
> R = 8.314
> gammaP = 0.00542
> betaP = 0.92
> gammaG = 0.0072
> betaG = 0 =>> Reading input =>> Reordering files
> Final order:
> 1. dna_rec.all.out: - =>> Reading files
> Reading dna_rec.all.out
> WARNING: Missing SROT for NM in 0 -> Taken from -1
> WARNING: Missing STOT for NM in 0 -> Taken from -1
> WARNING: Missing STRA for NM in 0 -> Taken from -1
> WARNING: Missing SVIB for NM in 0 -> Taken from -1

It seems that the nmode calculation failed and, thus, values for the
translational, ... entropies are missing for mm_pbsa.

My guess is that your system might be larger than what is considered the
default when compiling nmode. Comment the line "unlink $nmodeout;" in
mm_pbsa.pl and restart your calculation. Then check the
nmode.XXX.YYY.out file for error messages.

Best regards

Holger

>
> =>> Treat special
> parameters =>> Calc missing parameters =>> Calc average and stddev =>>
> Print output to dna_statistics.out
> 

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