# [AMBER] General question about MM-PB(GB)SA

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Sat, 7 Mar 2015 09:26:14 +0330

Dear amber users

I am doing MM-PBSA calculation for my protein-ligand system based on TUTORIAL
using AmberTools 14 (MMPBSA.py).

I have some general question:

1) Should I use all of the frames in solvated complex trajectory? Binding
delta G is different in various selections of frames. Is there a criterion
for selection of frames for MM-PBSA and MM-GBSA calculation (startframe and
endframe)? I have 2000 frames, what is your suggestion?

2) I calculated the binding free energy of my complex (protein-ligand) +
Quasi-harmonic entropy for one frame of trajectory:

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
-------------------------------------------------------------------------------

Since 1- Delta G = Delta H - T * Delta S and 2- Temperature is 298.15 K in
this calculation, thus

18.4960 = -2.3414 - 298.15 * Delta S, ===> Delta S = 0.069 kcal/mol.K

Is my consideration true?

3) I calculated 1- the binding free energy of my complex (protein-ligand)
for one frame of trajectory and 2- I calculated entropy of my complex
(protein-ligand) using Normal Mode Analysis for the same frame:

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

There are following in output file:

All units are reported in kcal/mole.
All entropy results have units kcal/mol (Temperature is 298.15 K).

How to use and combine DELTA S total (-3.5378) with DELTA TOTAL (-2.3414)?

Delta G = Delta H - T * Delta S

Delta G = (-2.3414) - (-3.5378)

Is my consideration true?

Best wishes,
Atila
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Received on Fri Mar 06 2015 - 22:00:02 PST
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