Yep will be thankful for everyone for any help!
E.g
1) string form the standart decomposition output- > the average energy is -1.230
TYR 234 | R TYR 234 | 0.000 +/- 0.000 | -1.525 +/- 0.696 |
-0.090 +/- 0.635 | 0.533 +/- 0.624 | -0.147 +/- 0.076 |
-1.230 +/- 0.694
2) dynamics of the energy (last column) along all snapshots from the
trajectory from the detailed log produced by -deo flag
2015-05-18 19:27 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
> _______________________________________________
> 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
Received on Tue May 19 2015 - 05:30:03 PDT
