> On Mar 8, 2015, at 8:22 AM, Atila Petrosian <atila.petrosian.gmail.com> wrote:
>
> Dear Jason
>
> Thanks for your answer.
>
> You are right. One frame for quasi-harmonic entropy does not make sense. I
> used one frame only for practic.
> Based on your suggestion, I will use 1/10th of those frames for MM/GBSA,
> MM/PBSA and quasi-harmonic entropy calculation.
>
> But I have 3 questions. My main problem is in reporting data obtained.
>
> 1) For example, (in quasi-harmonic) if we suppose my outputs for 1/10th of
> those frames are as follows,
>
> What is EDISPER?
This is part of the non-polar solvation free energy (it is the *attractive* part, or the dispersion interaction, between solvent and solute). It is part of the new “inp=2” non-polar solvation free energy model employed by PBSA. If you set inp=1, you get the more familiar ESURF/ENPOLAR that is a simple, repulsive scaling of the SASA.
>
> Energy Component Average
> --------------------------------------------
> BOND -0.0001
> ANGLE 0.0000
> DIHED -0.0000
> VDWAALS -22.8383
> EEL -6.8608
> 1-4 VDW 0.0001
> 1-4 EEL -0.0000
> EPB 18.8155
> ENPOLAR -15.1933
> EDISPER 23.7355
>
> DELTA G gas -29.6991
> DELTA G solv 27.3577
>
> DELTA TOTAL -2.3414
>
> -------------------------------------------------------------------------------
> Using Quasi-harmonic Entropy Approximation: DELTA G binding = 18.4960
> -------------------------------------------------------------------------------
>
> 2) If I want to report the obtained data (for example above),
> How to report those?
>
> Delta Eele -22.8383
> Delta Evdw -6.8608
> ===>
> DELTA G gas -29.6991
>
> and
>
> Delta G PB 18.8155
> ENPOLAR -15.1933
> EDISPER 23.7355
> ===>
> DELTA G solv 27.3577
>
> Is Delta G bind -2.3414 or 18.4960?
Assuming the quasi-harmonic entropy calculation is *good* (which it won’t be for only 1 frame), then the free energy computed by MM/PBSA is 18.4960.
>
> If my manner or comsideration is not true, please tell me how to report our
> data.
>
> 3) In last line of the output related to tutorial:
>
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm
>
> There is note: NOTE: All entropy results have units kcal/mol. (Temperature
> has already been multiplied in as 300. K).
>
> How to consider other temperatures in mmpbsa.in file to calculate entropy
> using normal mode analysis?
Not easily. You need to modify source codes to change the temperature. The vibrational and rotational entropies are computed via statistical mechanical formulae that assume a particular temperature (and for quasi-harmonic entropies, you really need to use the temperature that the simulation was run at). And last time I checked, this temperature was hard-coded directly into the program, so you would need to change the original source code and recompile, as well as modify the temperature variable in MMPBSA.py, in order to try a different temperature.
>
> 4) For example, (in normal mode) if we suppose my outputs for 1/10th of
> those frames are as follows,
>
> Energy Component Average
> ----------------------------------------------
> BOND -0.0001
> ANGLE 0.0000
> DIHED -0.0000
> VDWAALS -22.8383
> EEL -6.8608
> 1-4 VDW 0.0001
> 1-4 EEL -0.0000
> EPB 18.8155
> ENPOLAR -15.1933
> EDISPER 23.7355
>
> DELTA G gas -29.6991
> DELTA G solv 27.3577
>
> DELTA TOTAL -2.3414
>
>
> Entropy Term Average
> ----------------------------------------------
> Translational -12.1100
> Rotational -8.7200
> Vibrational 17.2921
>
> DELTA S total= -3.5378
>
> How to report our data?
>
> Delta Eele -22.8383
> Delta Evdw -6.8608
> ===>
> DELTA G gas -29.6991
>
> and
>
> Delta G PB 18.8155
> ENPOLAR -15.1933
> EDISPER 23.7355
> ===>
> DELTA G solv 27.3577
>
> Is -3.5378 equal to Delta S or T*Delta S?
The output file says, as you’ve pointed out, that all entropies have temperature already multiplied in as 300 degrees, and is in units of kcal/mole. So -3.5378 is T*deltaS
> Is Delta G bind -2.3414 - (-3.5378)?
Yes -- the output file should also give you this combined value (it says something like: Using Normal Mode Entropy Approximation: DELTA G binding = ...)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Mar 08 2015 - 19:00:02 PDT
