constraints on zinc ions

From: Wei Liu (wei.liu_at_biosci.ki.se)
Date: Mon May 28 2007 - 07:42:17 CDT

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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