Simulation of metalo-binding proteins

From: James Starlight (
Date: Wed Nov 23 2016 - 13:52:38 CST

Dear NAMD users!

I would like to perform brute force MD simulation of some oligomeric
water-soluble protein, where each monomer has several Cu2+ ions buried
within the binding pockets. Could you suggest me some template of the
script used for the preparation and parametrizartion routine (which
force fields in better for the ions) of such big protein including
metalo-ions and some other tutorial which can be usefull in my case?
For the simplicity, I can consider in my model ions as the non-bound
model, assuming that I'm interesting to study of the escaping on the
metalo-ions during the long MD simulation.

Thanks for help!


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