AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA nmode statistics

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Fri May 29 2009 - 00:13:34 CDT

Dear Dmitry,
Whatever i know you have to make some modifications in your
usr/local/amber10/src/mm_pbsa/ mm_pbsa_statistics.pm file. Follow this
procedure..
1- copy your mm_pbsa_statistics.pm as mm_pbsa_statistics.pm_old
2- Now modify in mm_pbsa_statistics.pm
 "ELRAELE" => [1,0,
  "EPB" => [1,0,
to "ELRAELE" => [0,0,
 "EPB" => [0,0,'
and
"PBNONPOL" => [1,0,

 "PBNONPOL" => [0,0,
I hope that it will run.
Regards
Kshatresh

2009/5/28 Dmitry Osolodkin <divanych_at_rambler.ru>

> Dear AMBER gurus,
>
> I have a problem with the analysis of nmode statistics during MM-PBSA.
> The .out files are generated (see attachment), but when trying to
> perform statistical analysis of them, I get the following message:
>
> > mm_pbsa.pl nmode.mmpbsa > nmode2.log
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> No data for 0+0 NM SROT 0
>
> This message appears also when I use the mm_pbsa_statistics.pl. What
> should I do to avoid this message and to perform normal calculation?
>
> Best regards,
> Dmitry Osolodkin
>
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o_at_org.chem.msu.su
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
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>
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