AMBER Archive (2009)

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

From: Dmitry Osolodkin (divanych_at_rambler.ru)
Date: Mon Jun 01 2009 - 08:12:15 CDT

Dear Ray,

The new results after the cleanup of output files are attached. The
difference between new and saved files is now rather small (but is it
negligible?).

I suppose that the real problem is inside the statistics module. I've
tried to calculate statistics from my out files in the separate
directory; the only suitable (i.e. generating non-empty stat.out file
containing the T*deltaS information) command was

mm_pbsa_statistics.pl 2 0 snapshot_statistics.in stat.out > stat.log 2>&1

The output is given in test.tar.gz. Is it a reasonable result?

> Also, as you noted, your nmode outputs are inconsistent with the saved
> files. So verify your installation of the amber10 executables by running the
> test cases in amber10/test to see whether you can pass those first.
Tests for nmode gave perfect results: the difference between the files
was only in the elapsed time estimation.

Dmitry.

>
> 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: Saturday, May 30, 2009 10:26 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MM-PBSA nmode statistics
>
> 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
>>>>
>>>> _______________________________________________
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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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