Calcium ion binding protein

From: vsweta_at_iastate.edu
Date: Tue Oct 21 2008 - 16:27:31 CDT

Hi all
I am trying to simulate a calcium ion binding protein using NAMD. From a
previously posted thread,

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8348.html

I understand I need to apply constraints to the calcium ions but I am unable to
figure out how to go about it.I have two segments one containing the protein and
the other containing the calcium ions. How do I reflect the covalent bonds
between the ions and the protein in the topology/parameter file ?

Thanks for your attention
Sweta

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:30 CST