I saw a paper refering a method to calculate the free energy of a SER covalent-orlistat ligand , the substrate orlistat is bound to SER amino acid.
But I have used to think that mmpbsa.py is only applied to calculate the binding free energy when a ligand and the protein seperately ,no bond exits in the ligand and protein.
I donnot know how to calculate the system when a ligand bond to protein. The system exits widely when you'd like to study the enzyme catalyse mechanism.
SO may someone give my some suggestions? Thanks!
The paper is :
Fako, Valerie E., Jian-Ting Zhang, and Jing-Yuan Liu
2014
Mechanism of Orlistat Hydrolysis by the Thioesterase of Human Fatty Acid Synthase. ACS Catalysis 4(10): 3444–3453.
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Received on Thu Apr 09 2015 - 20:00:02 PDT
