AMBER Archive (2004)

Subject: AMBER: how to check metal ion bonding ?

From: Venkata S Koppuravuri (
Date: Tue Apr 13 2004 - 14:13:52 CDT

Hi Amber Users,

I am trying to add Zinc to Cystine. I have followed the same procedure as
in Plastocyanin tutorial in the manual. Leap went fine without any error
messages. Before I start with minimization I want to make sure that all
the bonds with the Zinc are properly formed.

I have tried using Xleap, Sybyl, spdbv programs but the zinc ion and its
bonds were not shown.

Can someone suggest me a visualization program that I could use to check
the Zinc bonds.


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