AMBER Archive (2007)

Subject: RE: AMBER: Zinc-Histidine force field

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Nov 22 2007 - 13:01:30 CST

Antechamber can translate your QM output file to prepin file. Atomic charges
should be automatically fitted by a call to RESP within the program. But
torsion terms are a lot harder to tune if you can't find them. However, I'm
not sure you have to worry about torsion terms if you are using a covalent
zinc-binding interface. We were able to reproduce the vibration frequencies
of the zinc interface with zinc-related torsion terms set to zero.

 

All the 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: Thursday, November 22, 2007 4:06 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Zinc-Histidine force field

 

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?

Best,

mattia

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.
 
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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