This sounds like a specific error that is hard to track without looking at the files and doing troubleshoting. Besides as I am not experienced with decomposition logs, I am not able to help here much.
Maybe somebody else can better
Sorry
Vlad
On May 18, 2015 5:37:31 PM CEST, James Starlight <jmsstarlight.gmail.com> wrote:
>Thx again!
>Yes, I've just compare the plots in all cased the energy has been
>fluctuated around some positive (around +5) value which should not
>be correct in my case ( the averaged value around -1). I've made it
>using residue under my interests both from the COMPLEX and RECEPTOR
>arrays from the log using AWK.
>awk -v n=234 'BEGIN { OFS = FS = "," } $2 == n { print $NF }' ${file}
>> ${output}/${f_n}.log
>where 234 is the number of my residue which is alwais in the second
>column and the $NF is the value of the energy which is in the last
>column of the log.
>
> Is it possible that numbering of the residues in the detailed
>decomposition log is differs in comparison to its standard log?
>
>James
>
>2015-05-18 16:57 GMT+02:00 Vlad Cojocaru
><vlad.cojocaru.mpi-muenster.mpg.de>:
>> Please be also cautious about the fact that MMPBSA is not truly
>> decomposable (don't recall now a reference but we do provide one in
>our
>> paper). All in all, I'd say be careful about drawing any conclusions
>> from subtle differences in MMPBSA results in general ...
>>
>> Vlad
>>
>>
>> On 05/18/2015 04:31 PM, Vlad Cojocaru wrote:
>>> My opinion is that the question is "how much you can trust the
>>> estimation of the average ?". For that, you need the standard error
>of
>>> uncorrelated data ...
>>>
>>> The fluctuation around the average will not give you any information
>>> as the MMPBSA (in my understanding at least) is a method to estimate
>>> average dGs (or ddGs or dddGs for that matter)
>>>
>>> Vlad
>>>
>>> On 05/18/2015 04:23 PM, James Starlight wrote:
>>>> the question: is it it principle reasonable to compare fluctuations
>of
>>>> the dG for the specified residue (based on its decomposition data)
>for
>>>> several systems (e.g one receptor VS 10 different ligands) to make
>>>> some suggestions about contribution of the specified residue to the
>>>> molecular phenotype (e.g will ligand act as agonist or antagonist)?
>I
>>>> just compare several such profiles (taken from the last column of
>the
>>>> COMPLEX array from the detailed decomposition logs) for the residue
>>>> which made one of the dominant contribution to the AVERAGED binding
>>>> energy for all of my systems and didn't seen big difference between
>>>> them besides big fluctuations in each case (e.g values ranges from
>-1
>>>> to +15 being around +5 on average).
>>>>
>>>> James
>>>>
>>>> 2015-05-18 16:16 GMT+02:00 James Starlight
><jmsstarlight.gmail.com>:
>>>>> 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
>>>>>>>>>>> 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
>>>>>>>> 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
>>>>>> 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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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon May 18 2015 - 10:30:02 PDT
