Thanks for help again, Vlad!
However based on averaged values taken directly from standard
decomposition output of that system: the energy value of this residue
was around -1. So I suppose that in the detailed log the energy of
this residue are also should fluctuate around this averaged shouldn't
it ?
Regards,
J.
2015-05-18 15:53 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
> Sorry James, I did not use this output for decomposition analysis. I
> only used it for the overall energy analysis during the simulations. So,
> I don't know exactly if I can advise you on this ...
>
> The fact that you have positive values does not say much. Depending on
> the methodology you are using (MMPBSA allows lots of different
> alternative protocols) the values might be positive or negative. It may
> be that you need to look at all residues and search for those with the
> "least positive" contributions.
>
> We recently published a paper in Structure (by Felipe Merino et al 2014)
> in which we look at protein-DNA complexes. In that case we do get
> negative values for those residues which contribute positively but as
> soon as you change parameters and system, you may get all values
> positive. The paper has a detailed MMPBSA protocol and discusses some of
> the parameters used .. it may be worth reading. We are also preparing a
> follow-up with more detailed data on the MMPBSA (but its just in the
> making).
>
> Maybe somebody else may chime in here and help more than I can
>
> Best
> Vlad
>
>
>
> On 05/18/2015 03:15 PM, James Starlight wrote:
>> 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
>>>>>>>> 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
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>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> 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 - 07:30:07 PDT
