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

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Sun, 8 Mar 2015 15:52:16 +0330

Dear Jason

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:

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