AMBER Archive (2003)

Subject: Re: AMBER: nmode statistics

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Dec 18 2003 - 01:09:05 CST

kbyun_at_wesleyan.edu schrieb:
>
> Hi,
> I ran nmode for my protein-RNA system for the complex,
> ligand, and receptor for 3 snapshots. I do get the
> outputs in the files file_com.all.out, file_lig.all.out,
> and file_rec.all.out. I don't get the file that
> contains the statistics for the results
> file_statistics.out .
>
> The error message given is listed below. How can I get
> the statistics and what is wrong with my nmode run?

Comment the line "unlink $nmodeout;" in calc_NM in mm_pbsa.pl and rerun
the script. You should get the nmode out files then which will contain
further information about what might have gone wrong.

Best regards

Holger

>
> Thanks,
>
> Suzie Byun
>
> =>> 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. u1arna_wtup_com.all.out: -
> 2. u1arna_wtup_rec.all.out: -
> 3. u1arna_wtup_lig.all.out: -
> =>> Reading files
> Reading u1arna_wtup_com.all.out
> WARNING: Missing SVIB for NM in 0 -> Taken from -1
> WARNING: Missing STOT for NM in 0 -> Taken from -1
> WARNING: Missing SVIB for NM in 1 -> Taken from 0
> WARNING: Missing STOT for NM in 1 -> Taken from 0
> Reading u1arna_wtup_rec.all.out
> Checking CALC
> Reading u1arna_wtup_lig.all.out
> Checking CALC
> WARNING: Missing SVIB for NM in 0 -> Taken from -1
> WARNING: Missing STOT for NM in 0 -> Taken from -1
> WARNING: Missing SVIB for NM in 2 -> Taken from 1
> WARNING: Missing STOT for NM in 2 -> Taken from 1
> =>> Treat special parameters
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> Use of uninitialized value in multiplication (*) at
> /usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
> l
> ine 1258.
> =>> Calc missing parameters
> =>> Calc delta
> No data for 0+0 NM SVIB 0
>
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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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