[AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme

From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Date: Thu, 15 Oct 2020 22:11:54 +0530

Dear Users,

I am using MMPBSA.py for the first time to calculate the binding free
energy for my ligand bound enzyme system. After consulting manuals and
tutorials, I came to know that essentially I require four topology files:
one for the entire complex, one each for the receptor and ligand as well as
a solvated topology file for the complex as I have planned to execute MD
runs in explicit water. My enzyme system contains a tetra-coordinated zinc
ion at the active site and one of the sites is occupied by a crystal water
molecule (as ligand is not directly bonded to the metal center but in a
pocket near the active site). My question is whether I have to strip that
crystal water of from the pdb during complex topology formation or should I
retain it?

Thanks a lot,
Satyajit Khatua
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Received on Thu Oct 15 2020 - 10:00:02 PDT
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