[AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding

From: Vaibhav Jain <jain13.vaibhav.gmail.com>
Date: Sun, 17 Nov 2013 10:33:27 +0530

Hello everyone !!

I am wondering if MM-PBSA approach can be used for calculating the binding
free energy of a ligand with a macromolecule in the presence of other bound
identical ligands, which are in close proximity or stacked together.

System consisting of hyperbranched polymer in which 7 molecules of same
ligand are encapsulated. Now I wish to calculate the binding free energy of
each of the 7 bound ligand.

Please provide valuable suggestions in this direction and if possible
relevant articles based on similar concept.


*Warm Regards *
Vaibhav Jain (Ph.D. Scholar)
Dept. of Pharmacoinformatics
NIPER, S.A.S. Nagar (Punjab)
India, 160 062
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Received on Sat Nov 16 2013 - 21:30:02 PST
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