AMBER Archive (2009)

Subject: Re: [AMBER] About zinc parameters ?

From: steinbrt_at_rci.rutgers.edu
Date: Tue Nov 17 2009 - 04:35:24 CST

Hi,

> 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

if you modelled your Zn ion as a vdW sphere with a +2 charge, which would
be a reasonable first guess, it will tend to assume an octahedral ligand
shell around it. Basically, the charge is high enough to enforce a
'densest packing'-like arrangement of e.g. water molecules around a metal
center. Amber doesnt know anything about metal coordination geometries
unless you put that information in there by means of restraints, manually
added bonds or specifically designed metal-ligand units.

So, in my experience, if you want a tetrehedral Zn coordination, you will
have to build a model for it.

> 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

It is hard to comment on your solution if you dont detail what you did.
Did you just change the Zn parameters or build a Zn-containing unit or
manually added Zn-sidechain bonds or ... ? If you see a tetrahedral
Zn-coordination now, your models at least appears to do what it should,
right?

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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