AMBER Archive (2007)

Subject: RE: AMBER: Zinc-Histidine force field

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Nov 21 2007 - 11:30:21 CST

You can borrow some parameters from our following study on the p53 DNA
binding domain:

Molecular Dynamics Simulations of p53 DNA-Binding Domain, Lu, Q.; Tan,
Y.-H.; Luo, R., J. Phys. Chem. B., 2007, 111(39), 11538-11545.

In general, you'll have to do some QM calculations to get the parameters for
your specific system.

Best,
Ray

==========================================
Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528
Email: rluo_at_uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Mattia Mori - CERM
Sent: Wednesday, November 21, 2007 8:54 AM
To: amber_at_scripps.edu
Subject: AMBER: Zinc-Histidine force field

Dear amber users,
I'm trying to work with zinc protein  but I got some problems during the
parametrization with tleap.
When I bound the Zn ion to the NE2 of the three histidins with the command
"bond" and saveamberparm I get this error message:

Could not find bond parameters for : NB - Zn
Could not find angle parameters for: CV - NB - ZN
Could not find angle parameters for: CR - NB - ZN
......
parameter files was not saved

I think I've to built the .prep file and/or to modify the force field for my
protein but I don't know how to do that.
Do someone can tell me if there are some tutorials about? or where to find a
reliable forcefield fo MMPs protein?

thank you very much.

Mattia 

-- 

**-**-**-**-**-**-**-**-**-**-**-**-**
 
Mattia Mori, PhD Student
CERM - Centro di Risonanze Magnetiche
via L. Sacconi 6,,
50019 Sesto Fiorentino, FI
fax (+39) 055 4573914
tel (+39) 055 4573912
www.cerm.unifi.it

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