The question is only to what array from the decomposition log will be
what I'm looking for e.g I'm interesting in the energy dynamics of the
tyr- 234 residue of the receptor which have dominant contribution to
the binding so its energy (enthalpy) must be very negative.
In the first array which seems what I'm looking for I have only
positive values in all snapshots:
Complex:
Total Energy Decomposition:
Frame #,Residue,Internal,van der Waals,Electrostatic,Polar
Solvation,Non-Polar Solv.,TOTAL
1,234,110.877,-14.568,-87.049,-1.716,0.0200304,7.5640304
..
7,234,104.367,-14.487,-84.611,-3.651,0.01458,1.63258
..
16,234,116.053,-12.17,-87.315,-1.051,0.0055872,15.5225872
but in the last DELTAS array the values in the same positions are
slightly negative
DELTAS:
DELTA,Total Energy Decomposition:
Frame #,Residue,Location,Internal,van der Waals,Electrostatic,Polar
Solvation,Non-Polar Solv.,TOTAL
1,TYR 234,R TYR 234,0.0,-1.0,-1.313,1.901,-0.1018944,-0.5138944
..
16,TYR 234,R TYR 234,0.0,-0.291,-0.037,0.455,-0.094788,0.032212
..
35,TYR 234,R TYR 234,0.0,-0.92,0.216,0.161,-0.1295496,-0.6725496
also I have two rest arrays for the RECEPTOR and for the LIGAND. So
which one will be useful for me?
2015-05-18 14:37 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
> 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
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>>>>> _______________________________________________
>>>>> 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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>
> --
> 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 - 06:30:04 PDT
