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From: Jason Swails <jason.swails.gmail.com>

Date: Sun, 8 Mar 2015 21:40:24 -0400

*> 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

Date: Sun, 8 Mar 2015 21:40:24 -0400

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.

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.

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.

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

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Mar 08 2015 - 19:00:02 PDT

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