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From: Atila Petrosian <atila.petrosian.gmail.com>

Date: Sun, 8 Mar 2015 15:52:16 +0330

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?

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?

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?

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?

Is Delta G bind -2.3414 - (-3.5378)?

In most of paper in which solute entropy was calculated using nmode and

amber, T*Delta S is reported.

Excuse me for simple and basic question.

Any help will highly appreciated.

Best wishes,

Atila

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Mar 08 2015 - 05:30:02 PDT

Date: Sun, 8 Mar 2015 15:52:16 +0330

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?

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?

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?

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?

Is Delta G bind -2.3414 - (-3.5378)?

In most of paper in which solute entropy was calculated using nmode and

amber, T*Delta S is reported.

Excuse me for simple and basic question.

Any help will highly appreciated.

Best wishes,

Atila

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Mar 08 2015 - 05:30:02 PDT

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