HI
When I was working with Zn, I followed this tutorial. Hope this tutorial helps you
http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.php
Balajee
________________________________
From: Sayan Poddar via AMBER <amber.ambermd.org>
Sent: Saturday, August 5, 2023 2:29 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Question about Zinc ions
Dear AMBER developers and Users,
I have two Zinc ions bound to my protein structure in the cysteine-rich
domain with one histidine residue also involved in binding. I was preparing
the topology and coordinate files for the protein using tleap. Do I need to
do any special modification in the PDB or use any other forcefields for
zinc? I have used ff14SB and gaff2 forcefields for protein and ligands,
respectively and tip3p water model.
Thank you
--
*with regards*
*Sayan Poddar*
*PhD Research Scholar*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology Indore*
*India*
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Received on Sat Aug 05 2023 - 04:30:02 PDT
