AMBER Archive (2003)

Subject: AMBER: modelling a Ca binding site

From: Karsten Suhre (Karsten.Suhre_at_igs.cnrs-mrs.fr)
Date: Thu Aug 14 2003 - 04:36:53 CDT

Dear Amber users,

could anyone direct me to an example showing how to introduce a Calcium ion
into a protein simulation (i.e. the leap part - what files do I need, how to
name the CA and so on)?

To be somewhat more specific about my goal: I have a homology model of a
protein, with a predicted Ca binding site, and I know the approximate
co-ordinates of the Ca ion from the templates. What I would like to do is run
a minimization to get the Ca in place (by restraining all protein parts
except for the side chains involved in Ca coordination, perhaps varying those
that are involved), and as a second step do a dynamical simulation with and
without the ion to get an idea of its overall effect on the structure.

Any comments would be welcome,

Kind regards, and thank you very much in advance, Karsten. 

-- 
Karsten Suhre                  
Information Genomique & Structurale       
CNRS
F-13402 Marseille Cedex 20

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