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
>>>>
>>>> _______________________________________________
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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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>> _______________________________________________
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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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Received on Fri May 15 2015 - 05:00:02 PDT
