As the entropic term is missing in g_mmpbsa tool. We have to calculate the entropy of protein-ligand system for estimating binding free energy.
Dear Shubhandra,
Attached please find a chapter entitled " Calculating(binding(free(energies(for(
protein-carbohydrate(complexes" which covers the answer to your question.
Hoping this will be helpful,
Rafik
You can use g_covar and subsequently g_anaeig to get entropy of the system.
This short bash script analyses the H-bond occupancy from Gromacs MD trajectory.
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