Could you please send me off the list the 2 files ?
Vlad
On 05/19/2015 02:32 PM, James Starlight wrote:
> Yep will be thankful for everyone for any help!
>
> E.g
> 1) string form the standard 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
> 1,234,110.877,-14.568,-87.049,-1.716,0.0200304,7.5640304
> 2) dynamics of the energy along all snapshots from the
> trajectory from the detailed log produced by -deo flag look like
>
> 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
>
>
> and its for several snapshots in 3 column form:1- number of snapshot
> (1 col), 2- number of residue (2nd col), energy (last column)
>
>
> 1,234,7.5640304
> 2,234,8.1933352
> 3,234,14.5362168
> 4,234,11.3559576
> 5,234,4.1508616
> 6,234,7.3968288
> 7,234,1.63258
> 8,234,9.709776
> 9,234,7.6749752
> 10,234,9.3017696
> 11,234,12.0413344
> 12,234,9.4072816
> 13,234,8.7905704
> 14,234,7.3629904
> 15,234,13.2913608
> 16,234,15.5225872
>
> so the values are not the same and in dynamics are always very
> positive which looks wrong.
>
> James
>
> 2015-05-19 14:23 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> 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.
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> _______________________________________________
> AMBER mailing list
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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 Tue May 19 2015 - 06:30:02 PDT
