Hi,
Considering the zinc ion to be tetra-coordinated, you have to write
addAtomTypes { { "ZN" "Zn" "sp3" } { "S1" "S" "sp3" } { "S1" "S" "sp3" } { "S1" "S" "sp3" } { "S1" "S" "sp3" } }
Best,
Satyajit
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________________________________
From: Sayan Poddar via AMBER <amber.ambermd.org>
Sent: Monday, December 25, 2023 12:38:22 pm
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Query regarding preparation of protein system having zinc ion using ZAFF
Dear AMBER developers and Users,
My protein structure contains a zinc ion encircled by four cysteine
residues. The system preparation for simulation was conducted following the
provided tutorial.
http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.php
However, I have a question; the tleap file includes the following line
concerning atom type.
*addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } { "N2" "N" "sp3" } }*
#Add atom types for the ZAFF metal center with Center ID 4
The tutorial provides the naming convention for atoms in various systems.
I changed 'S3' to 'S1' in { "S3" "S" "sp3" } because my zinc ions are
surrounded by four cysteine residues. However, since these residues lack
nitrogen atoms, is it permissible to eliminate the portion { "N2" "N" "sp3"
} from addAtomTypes?"
So my final syntax would be like
*addAtomTypes { { "ZN" "Zn" "sp3" } { "S1" "S" "sp3" } }*
Is this right?
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 Mon Dec 25 2023 - 10:00:03 PST
