AMBER Archive (2009)

Subject: Re: [AMBER] About zinc parameters ?

From: Sally Pias (
Date: Tue Nov 17 2009 - 11:38:29 CST

You may be interested in the "cationic dummy atom" approach developed
by Yuan-Ping Pang and colleagues:

Pang YP. Successful molecular dynamics simulation of two zinc
complexes bridged by a hydroxide in phosphotriesterase using the
cationic dummy atom method. Proteins: Structure, Function, & Genetics
2001 Nov 15; 45(3):183-189.

Pang YP, Xu K, Yazal JE, Prendergas FG. Successful molecular dynamics
simulation of the zinc-bound farnesyltransferase using the cationic
dummy atom approach. Protein Sci 2000 Oct; 9(10):1857-65.

Dr. Pang has AMBER force field parameters for this model available for
download on his website:

Sally Pias

On Tue, Nov 17, 2009 at 3:35 AM, <> wrote:
> 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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> AMBER mailing list

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