Check out the method section in the following paper: Molecular Dynamics of
p53 DNA Binding Domain, *J. Phys. Chem.*, 111:11538-11545, 2007.
All the best,
Ray
2009/12/30 xuemeiwang1103 <xuemeiwang1103.163.com>
>
> 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
> is form octahedron with this 4 residues,the result seems not fit in with
> my initial thought.I thought it may be relate with the Zn parameters.I fond
> the non-bonded model fails to give the correct coordination number by
> reading the reference.In order to solve this ,I want to addopt the bonded
> approach for the Zinc ion.I extracted the active site as a model ,and opted
> it by Gaussian .But I don't konw how to get the force constants bettwen two
> Atoms ,could someone tell me ,thank you very much!
>
>
>
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Received on Thu Dec 31 2009 - 18:30:03 PST
