WAY: Binging-free energy with entropy correction

Izaz Monir Kamal

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Dec 19, 2021, 12:16:22 AM12/19/21

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Dear Sir,

I have some Protein-Ligand comlexes, these complexes undergo simmulution by GROMACS.

Now i am trying to calculate Binging-free energy with entropy correction, Sir i am totally confused about which input file can i used for this calculation.

If you provide me that input i will be grateful for you.

Regards

Izaz

marioe911116

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Dec 19, 2021, 12:43:13 AM12/19/21

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Hi Izaz!

you can use either this (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/Interaction_Entropy/) for Interaction Entropy or this (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/nmode/) for normal mode. Take into account that nmode is computationally very expensive compared to Interaction entropy...

cheers!

Mario E.

Izaz Monir Kamal

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Dec 19, 2021, 2:51:25 AM12/19/21

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Thank You Sir,

Sir, Previously i used g_mmpbsa (Kumari et al (2014) g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model. 54:1951-1962) for protein ligand complexes where binding free energy value highly drifted, it take 8 hours for a complex run.

While gmx_MMPBSA Entropy correction with binding free energy value takes about 5 minute(Example run).

Sir now i want to produce my result (input file: GROMACS simulated Protein-LIgand Complex) through gmx_MMPBSA, what will be the complete step or procedure?

Sir my aim1: Most accurate binding free energy calculation which is computationally less expensive.

Sir my aim2: Most accurate binding free energy with entropy calculation (entropy correction)

Sir Your above Two suggestion:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/Interaction_Entropy

or

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/nmode/

These two suggestion can enough to solved my ( my aim1+ my aim2) problem?

Regards & Thanking You

Izaz

Mario Ernesto

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Dec 19, 2021, 3:07:16 AM12/19/21

to Izaz Monir Kamal, gmx_MMPBSA

Go over the tutorials I mentioned before and they state exactly what's needed for running the calculations...

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Izaz Monir Kamal

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Dec 19, 2021, 4:01:59 AM12/19/21

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Sir,

Please help me.

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/Interaction_Entropy/

This tutorial can i used for binding free energy as well as entropy calculation.

Regards

Izaz

marioe911116

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Dec 19, 2021, 5:35:16 AM12/19/21

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yes, it reports the binding free energy as the sum of enthalpy and entropy

Izaz Monir Kamal

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Dec 19, 2021, 5:50:53 AM12/19/21

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Thank You Sir.

Regards

izaz

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