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
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Received on Wed May 13 2015 - 09:00:05 PDT
