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
>>>>
>>>>
>>>> _______________________________________________
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>>> _______________________________________________
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>>
>> --
>> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon May 18 2015 - 05:00:03 PDT
