Re: zinc parameter?

From: Fangqiang Zhu (
Date: Mon Nov 17 2003 - 18:24:08 CST


Do the zinc ions have covalent bonds with the protein? If not, then things are very
simple, because there're only non-bond interactions involved, and the CHARMM
force field already provides all the parameters needed. However, if the zinc ions are

indeed involved in covalent bonds, you'll need more parameters and they're
not in the standard CHARMM force field (as far as I know). In that case it will be

Zhu, Fangqiang wrote:

> Dear sir,
> I want to use NAMD program to do a MD calculation on an enzyme with two zinc
> ions. I see CHARMM topology file has include zinc ion. However when I generate psf
> and pdb file, there is only one zinc ion. How should I solve this problem?
> As for a small ligand, though the NAMD tutorial said MOE and SPARTAN can
> generate force field for novel system, I can't get MOE because it isn't free. As
> to SPARTAN, I am not quite clear on how to genarate those parameters.I can only
> find charge in the output file.
> As we know, there are many parameters for a molecule such as bond,angle,dihedral
> angle,etc, need I calculate them with Spartan ,then type them in topology and
> parameter file in NAMD program? If yes, it is so complicated. Whether is there
> software which can generate topology and parameter file for NAMD program?
> Thanks !

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