AMBER Archive (2009)

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

From: Dmitry Osolodkin (divanych_at_rambler.ru)
Date: Sat May 30 2009 - 12:25:46 CDT

Dear Ray,

If you mean bugfix 17 -- yes, I patched it. The results of make
test.Nmode are in the attached file; briefly, the error is still
present, but outfile (very different from saved version) is generated.
Tests of Generation, Stability, Binding and Decomposition produce
results identical with the examples, so the problem is located in the
nmode module.

Ray Luo wrote:
> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>> _______________________________________________
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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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