AMBER Archive (2009)

Subject: [AMBER] Zinc parameters?

From: xuemeiwang1103 (
Date: Wed Dec 30 2009 - 21:37:21 CST

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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