Once you have those data in a file, you can use any scripting language
(python, perl, tcl, awk) to sort it in any way you want ...
Vlad
On 05/18/2015 01:38 PM, James Starlight wrote:
> btw what I've found in the log produced by -deo is that all data has
> been sorted in accordance to the frame number
> i.e
>
> Total Energy Decomposition:
> Frame #,Residue,Internal,van der Waals,Electrostatic,Polar
> Solvation,Non-Polar Solv.,TOTAL
>
> What would be most trivial way to sort all of those data primarily
> based on the residue number ? In fact each time I'd like only to look
> on the dynamics (as the function of the frame number from 1st column)
> of the total energy (last column) of the one chosen residue (taken
> from the 2nd column).
>
> Thanks for any ideas!
>
> James
>
> 2015-05-15 13:30 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> Thanks so much, Vlad!
>> -eo and -deo flags seems like what I was looked for assuming that I'd
>> like also to look into enthalpy fluctuations for specified residues of
>> the decomposition output.
>>
>> Regards,
>>
>> James
>>
>> 2015-05-13 17:47 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
>>> If I understand your problem correctly, it can be solved simply by
>>> specifying an output file of your wish using the "-eo" option (page 632
>>> amber 15 manual) ... This will store all energy terms for all frames
>>> analyzed ... Did your try this ? Isn't it what you want ?
>>>
>>> Vlad
>>>
>>>
>>> On 05/13/2015 05:26 PM, James Starlight wrote:
>>>> So no new options (like specified values for verbose or dec_verbose)
>>>> should not be added to the inputs? I really didn't find information
>>>> about dumping of the outputs within the manual. Into which file should
>>>> I look?
>>>>
>>>> Thanks!
>>>>
>>>> James
>>>>
>>>> 2015-05-13 16:04 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
>>>>> You can dump the output into a file using the "-eo" option (see
>>>>> MMPBSA.py part of the AMBER manual).
>>>>>
>>>>> Best
>>>>> Vlad
>>>>>
>>>>>
>>>>>
>>>>> On 05/13/2015 03:55 PM, James Starlight wrote:
>>>>>> Dear Amber users!
>>>>>>
>>>>>> Based on the mmgbsa outputs (including both dG and decomposition
>>>>>> outputs) I'd like to monitor fluctuations of the total dG over the
>>>>>> trajectory (and possible to see both dH and dS dynamics). Also I'd
>>>>>> like to do the same on the per-residue basis (E.g to see how dH
>>>>>> fluctuate for several chosen residues). I'd be thankful if someone
>>>>>> provide me what flags should I activate in the mmgbsa input file and
>>>>>> what output files will contain that information?
>>>>>>
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> James
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>>
>>>>> --
>>>>> Dr. Vlad Cojocaru
>>>>> Computational Structural Biology Laboratory
>>>>> Department of Cell and Developmental Biology
>>>>> Max Planck Institute for Molecular Biomedicine
>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Mon May 18 2015 - 06:00:03 PDT
