AMBER Archive (2009)

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

From: Ray Luo (ray.luo_at_uci.edu)
Date: Fri May 29 2009 - 13:01:36 CDT

Dmitry,

Have you patched the amber10 bugfix for mmpbsa? If so, can you reproduce all
the examples for mmpbsa? Let's make sure your installation is okay first ...

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Dmitry Osolodkin
Sent: Friday, May 29, 2009 3:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MM-PBSA nmode statistics

Dear Kshatresh,

Unfortunately, your suggestion doesn't help. The problem is still
present. BTW, the usage of PBNONPOL is commented throughout the script.

Best regards,
Dmitry

Kshatresh Dutta Dubey wrote:
> 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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-- 
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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