Re: AMBER: Zinc-Histidine force field

From: Mattia Mori - CERM <>
Date: Thu, 22 Nov 2007 13:06:20 +0100
thank you for the paper, I'm reading it. I'm running QM calculation on the zinc-histidine system to calculate the charge, but what I don't know is how to incorporate them in a new force fields and how to calculate torsional parameters? I'll get them in the gaussian ouyput?
Should I modify manually the force field or is better to use antechamber to obtain the .prepi for the small system?



Ray Luo ha scritto:
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.


Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528

-----Original Message-----
From: [] On Behalf Of
Mattia Mori - CERM
Sent: Wednesday, November 21, 2007 8:54 AM
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 Mori, PhD Student
CERM - Centro di Risonanze Magnetiche
via L. Sacconi 6,,
50019 Sesto Fiorentino, FI
fax (+39) 055 4573914
tel (+39) 055 4573912
----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to Received on Sun Nov 25 2007 - 06:07:18 PST
Custom Search