Dear all, I am currently in bioinformatics, as an undergraduate.
In md simulation, I calculated binding free energy of protein-ligand complex model by MM/PBSA. As MM/PBSA method has some challenges such as entropy, I am trying to integrate entropy with MM/PBSA using "Interaction entropy". But, I have some diffculty in how to handle this problem because of Boltzmann constant.
Do I have to calculate it through some mathematical approach or equations?
or If I have to add these large scales without conversion, can you recommend some programs dealing with these exponential scales?
Hi Il Kwon Cho,
It is possible to calculate the entropy by nmode analysis (AMBER).
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm
Alternatively you could check this paper which details the theory behind "interaction entropy".
Article Interaction Entropy: A New Paradigm for Highly Efficient and...
BEERT is another option.
Article Efficient Approximation of Ligand Rotational and Translation...
The 'interaction entropy' is included implicitly in the average electrostatic and non-electrostatic interaction energies between the ligand and its surrounding environment.
check gmx_MMPBSA, a new tool aid to perform end-state free energy calculations with GROMACS files. Things you can do with gmx_MMPBSA:
-binding free energy with different solvation models (PB, GB, or MM/3D-RISM)
-stability
-alanine scanning
-entropy corrections
-binding free energy decomposition
gmx_MMPBSA has been written in Python3.8 and is entirely based on AMBER’s MMPBSA.py, a widely used tool for streamlining end-state free energy calculations. The program is freely available (test files and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
hth!
I really appreciate your reply. As interaction entropy was not appropirate in my membrane complex system, I applied nmode as an alternative.
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