How to calculate the final binding free energy

li tao

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Nov 13, 2021, 10:39:24 PM11/13/21

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Dear mariosergi,

The following results after gmxmmpbsa calculation. I want to know how to calculate the final binding free energy.

IF the binding free energy= DELTA G gas + DELTA G solv + VDWAALS + EEL + EGB + ESURF. Besides, I want to know the meaning of EEL , EGB, and ESURF. thanks a lot.

With my best regards！

Differences (Complex - Receptor - Ligand):

Energy Component Average Std. Dev. Std. Err. of Mean

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

BOND 0.0000 0.0001 0.0000

ANGLE -0.0000 0.0000 0.0000

DIHED -0.0000 0.0000 0.0000

VDWAALS -16.4868 2.3846 0.0337

EEL -8.3599 2.6265 0.0371

1-4 VDW -0.0000 0.0001 0.0000

1-4 EEL 0.0000 0.0001 0.0000

EGB 13.6325 2.8689 0.0406

ESURF -2.3801 0.3651 0.0052

DELTA G gas -24.8467 3.5391 0.0500

DELTA G solv 11.2524 2.6808 0.0379

DELTA TOTAL -13.5943 2.1059 0.0298

Mario Ernesto

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Nov 14, 2021, 4:55:07 AM11/14/21

to li tao, gmx_MMPBSA

Hello there!

Well, technically what you got here is the effective energy, in other words the enthalpic part of the binding free energy. The equation is as follows:

DELTA TOTAL = DELTA G gas + DELTA G solv

DELTA G gas = BOND + ANGLE + DIHED + EEL + VDWAALS

DELTA G solv = DELTA EGB + DELTA ESURF

EEL - electrostatic component of the internal energy

EGB - polar component of the solvation energy (in this case is calculated using Generalized Born model)

ESURF - no polar component of the solvation energy (proportional to the Solvent Accesible Surface Area of the solute)

For a more detailed analysis of the equation and terms, check our publication (https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645)

Cheers!

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veena sukumaren

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Jan 12, 2022, 8:40:18 AM1/12/22

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Sir,

I have done the dynamics simulation of the same complex in GROMACS 2018version and binding energy calculation by g_mmpbsa. There I got -82.13 ± 37.17KJ/mol. here it's -5.405kcal/mol.

actually, I have done 50ns simulation at the beginning and communicated to a journal. But they asked me to do it in 100ns. now due to rush and lack of space at the server, I tried it in gromacs 2021 and followed by GMX_MMPBSA.

So my doubt is how to correlate these two values

veena sukumaren

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Jan 18, 2022, 2:32:29 AM1/18/22

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So shall I go ahead with this result.

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marioe911116

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Jan 18, 2022, 2:39:53 AM1/18/22

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I personally prefer using MM-PB(GB)SA method for relative binding free energy calculations rather than absolute ones... the question you ask, you and only you are the most qualified person to answer the question... we guarantee that gmx_MMPBSA works properly, now it's your job to determine whether it fits your needs or not...