AMBER Archive (2009)

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

From: Dmitry Osolodkin (divanych_at_rambler.ru)
Date: Fri May 29 2009 - 05:53:27 CDT

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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