AMBER Archive (2003)

Subject: RE: AMBER: Zinc parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 18 2003 - 15:26:49 CST

Dear Annette,

The best parameters I have found for Zinc bonded to cysteine and histidine
are those of Ryde. See this paper:

Ryde, U., Proteins: Structure, Function and Genetics, 21:40-56 (1995)

Regarding the website the link is now:
http://amber.scripps.edu/0Net/index.html

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Annette Höglund
Sent: 18 November 2003 05:19
To: amber
Subject: AMBER: Zinc parameters

Dear Amber users,

I am running simulations on a protein that contains Zn ions, and I am
missing a few parameters needed in leap for the Zinc ion. The zinc is
being coordinated by two HIS and two CYS, more specifically HID and CYX.
I have not been able to view the
www.amber.ucsf.edu/amber/ONet/index.html, has it been moved to a new
location? The parameters I need are for the frcmod file follow below.

Thanks in advance!

Annette
.......................................................
MASS:
?

BOND:
S-Zn
NB-Zn

ANGLE:
S-Zn-S
S-Zn-NB
CT-S-Zn
CV-NB-Zn
NB-Zn-NB
CR-NB-Zn

TORSION/DIHE:
S-Zn-S-CT
S-Zn-NB-CR
S-Zn-NB-CV
CT-S-NB
CV-NB-Zn-NB
NB-Zn-NB-CR
NB-Zn-NB-CV
CR-NB-Zn-NB
CT-S-Zn-NB

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