Re: coordination chemistry with NAMD

From: L. Michel Espinoza-Fonseca (
Date: Wed Aug 02 2006 - 14:34:00 CDT

Hi Sharma,

About your question, I think you can do what you're inquiring about. I
can suggest some "quick and dirty" procedures you could use for what
you want.

1) I don't think there are such parameters (Zn2+ coordinated with
His). However, you could obtain them by several QM runs using the tool
Paratool, a nice plug-in for VMD. I have to warn you that this is not
very quick and easy -wow! now I'm contradicting myself :)-

2) You can check out in the topology files if there are topologies for
Zn2+ (right now I don't remember if such parameters are included in
the standard versions of the CHARMM ff). If there are such parameters,
then you can build your system Zn2+ -His. You have to be very careful
about the protonation state you'll assign to His.

3) If you already got your system, you should minimize your system
containing the "coordinated" Zn-His system and see how it behaves.

4) finally, for your simulation purposes, you can apply "constraints"
to your "virtual" coordination bond between Zn and His. You can test
different constraints (from 300 to 600 kJ/mol, for example) and see
which one satisfies you more. You can assign such constraints with

As I told you, this is what I would do to alleviate the pain caused by
the rigorous parametrization process. I hope it helps!

Good luck!

2006/8/2, Gaurav Sharma <>:
> Hi All,
> I want to simulate Zinc ion - Histidine coordination bonding using NAMD.
> Is it possible to simuate this bond with the available parameters for
> Zn+2 ion in the Charmm force-field?
> Can this bond be modeled as a covalent bond with some tweaking of the
> parameters?
> A more generic question would be: Is it possible to simulate
> coordination bonds between metal ions and protein?
> Thanks for your help.
> Gaurav

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