Re: Simulation of metalo-binding proteins

From: Jérôme Hénin (
Date: Wed Nov 23 2016 - 14:11:44 CST

Hi James,

To answer your question, allow me to start with this hypothetical request:
"I wish to tighten a bolt using a hammer. Can you tell me the exact
sequence of movements I need to do with my hammer to tighten this bolt?".

The answer, of course, is that you're looking at the wrong tool for the
job. In short, the force fields implemented in NAMD suck at describing
copper-protein interactions in any detail - which is what you want if
you're interested in metal unbinding. There are special force fields for
that, but they are more complex, and not implemented everywhere (see e.g.
ligand field molecular mechanics).

Or you may want to look into QM/MM simulations:


On 23 November 2016 at 20:52, James Starlight <>

> 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!
> James

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