Dear amber users
I am doing MM-PBSA calculation for my protein-ligand system based on TUTORIAL
A3: MM-PBSA <http://ambermd.org/tutorials/advanced/tutorial3/index.htm>
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
