Re: constraints on zinc ions

From: Peter Freddolino (
Date: Mon May 28 2007 - 08:58:19 CDT

Hi Wei,
Could you be a little more detailed about how you had set up your zinc
ions? If you put harmonic constraints on their positions, and they still
move, that probably means the constraints aren't being applied
correctly. You may also want to double check that the system has been
properly relaxed prior to allowing motion of the protein and zinc ions.
Also, are the cysteines complexing your zinc ions deprotonated?

The type of constraint you're asking about at the end will be available
in the next release of NAMD, but is currently only available in the CVS
version. It sounds like there are a couple other things that should be
tried first, though.


Wei Liu wrote:
> Dear all,
> I am performing a simulation of a protein-DNA complex in the NPT
> ensemble. My protein contains a zinc finger domain that is believed to
> be crucial in DNA binding. There is one zinc ion in each subunit and
> six in total. During simulation, however, the zinc ions always tend to
> fly from their coordinated sites and go into the solvent, even through
> the harmonic constraints have been defined on them. I could fix the
> position of these zinc ions, but the whole zinc finger motif will be
> much less mobile in MD simulation. This is definitely not my
> expectation. On the contrary, I expect the zinc finger domain will
> move closer to DNA. Does anyone know if I can define a distance
> restraint, for example to define the distance between an atom zinc
> and the atom SD in a cysteine residue less than 2.5 angstrom, in
> namd? That is, distance ("name ZN", "resid 171 and name SD") <= 2.5
> Thanks in advance
> Regards
> Wei

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