# Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 19 May 2015 14:32:42 +0200

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
>
>
>> 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
>>
>> 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
>>>
>>>> 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 ...
>>>>
>>>>
>>>>
>>>> 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)
>>>>>
>>>>>
>>>>> 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
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 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
>>>>>>>>>> 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 ...
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 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>:
>>>>>>>>>>>> -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
>>>>>>>>>>>>> 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 ?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>> You can dump the output into a file using the "-eo" option
>>>(see
>>>>>>>>>>>>>>> MMPBSA.py part of the AMBER manual).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>
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>>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
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Received on Tue May 19 2015 - 06:00:02 PDT
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