AMBER Archive (2009)

Subject: [AMBER] About zinc parameters ?

From: xuemeiwang1103 (
Date: Tue Nov 17 2009 - 02:52:56 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 (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!


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