Hi,
Yes, the water molecule is occupying one of the ligand-binding sites of the
tetra-coordinated zinc ion. So, should I have to retain it?
Thanks,
Satyajit Khatua
---------- Forwarded message ---------
Date: Thu, 15 Oct 2020 14:29:26 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Query about using MMPBSA.py to calculate the
binding free energy for a ligand bound enzyme
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20201015182926.gauxkiodkpvbqfba.rulx-presler-l.rad.rutgers.edu>
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On Thu, Oct 15, 2020, SATYAJIT KHATUA wrote:
>
>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?
I'm a little confused: is the water one of the four ligands for the
"tetra-coordinated" zinc?
Basically, if a water is "sructured" (likely to stay in one place),
you should retain it, i.e. treat it as part of the protein, not part of
the solvent.
...dac
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Received on Fri Oct 16 2020 - 03:30:02 PDT
