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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

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Mar 06 2015 - 22:00:02 PST

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

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Mar 06 2015 - 22:00:02 PST

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