AMBER Archive (2009)

Subject: Re: [AMBER] About zinc parameters ?

From: Jason Swails (
Date: Tue Nov 17 2009 - 09:17:23 CST


I just wanted to bring your attention to one small detail. You said you are
using leaprc.ff99, which is known to have serious issues dealing with
backbone torsion angles. I believe it unfairly biases proteins toward
adopting alpha-helix secondary structures (it unfairly favors the torsion
angles responsible for that secondary structure). leaprc.ff99SB uses all of
the same parameters except for these two torsion angles that it fixes, so I
would suggest using that force field unless you have a strong reason for
using the first.

Good luck!

2009/11/17 xuemeiwang1103 <>

> Dear Amber users:
> I am working on simulation of enzyme protein.The aim is to study the zinc
> active site .Fist,the zinc ion in my pdb file can't be recgonized by
> LEAP(BTW,Iam use Amber9 and leaprc.ff99).So I reference the Amber
> Archive,following the Dr Ross walker's suggestion,I solved this problem
> ,everything seems ok .But when I have done my simulation ,I found the zinc
> which should be formed 4 coordination bonds with 4 residues of the protein
> (His331 N ,His351N,GLU451 O1, ACT OXT) is form octahedron with this 4
> residues( His331 N ,His351N, GLU451 O1,O2, ACT O OXT),the result seems not
> fit in with my initial thought.I thought it may be relate with the Zn
> parameters I creat which seems not consider the zinc surroundings
> .Accidentally,I found the Amber Force Parameters for Terahedron-Shaped Zinc
> Divalent Cation in the Amber Home Page as CaDA ,I used this parameters ,now
> the result seems right .But I am not sure wether it's right to solve the
> problem like this ,could someone help me ?your comments ara highly
> appreciate!
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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