AMBER Archive (2004)

Subject: AMBER: prep file for zinc finger

From: Wen Li (liw_at_wadsworth.org)
Date: Wed Jan 21 2004 - 16:02:54 CST

Dear AMBER users,

I was hoping that you could help me the following question about
preparation file for zinc ions:

The X-ray structure that I am going to simulate on includes zinc finger
motif, and the crystal gave the coordinates of the Zn atoms. I noticed
that the parameters for Zn(2+) have been included in parm99.dat. But I
guess that I need to make bond connection between zinc to sulfides in
CYS residues. Based on the tutorial of Plastocyanin/ion/water, the
bonding information should be included in preparation .in file
(coordinate matrix file). I wonder: (1) if such an input file of modified
CYS for zinc finger has been there that can be directly used? (2) If I
should create the file on my own, should I modify the input file for CYS by
filling the geometry based on the crystal structure? (3) What are the
values of charge for the zinc and sulfide atoms?

I appreciate your help.

Wen
 

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