Re: coordination chemistry with NAMD

From: Jan Saam (
Date: Fri Aug 04 2006 - 03:16:28 CDT

Hi Gaurav,

when you are modelling the coordination bonds using nonbonded
interactions you'll most likely end up with a crooked geometry of the
complex because the VDW radii are not optimized for the interaction of
two adjacent ligands. But if you know the complex geometry, e.g.
tetrahedral or octahedral you can adjust these parameters accordingly.


Gaurav Sharma wrote:
> Hi Meredith, Nitin, Michel and others,
> Thanks for your response, they have been all very insightful. So it
> seems there are two possible ways to simulate metal ion - protein
> interactions:
> 1. By artificially creating a bond between the cation and the nitrogen
> atom of His residue and updating the force-field with the new
> parameters for the bond.
> 2. By treating the coordination bond as a non-bonded interaction and
> simulating it with the already available parameters in the charmm ff.
> My goal is to study the conformational changes induced by divalent
> ions in proteins. So I guess the best procedure for me would be to
> place the metal ion near the His residues and simulate the system
> assuming that the non-bonded interactions are sufficient to simulate
> the dynamics involved. I hope this is a simple and effective way to
> solve my problem. Please let me know of your thoughts for the same.
> Also does anyone know of similar parameters for divalent ions other
> then Zn (such as Ni+2, Cu+2 etc.)
> Thanks again for your help.
> Gaurav
> Meredith Foley wrote:
>> Hi Gaurav-
>> There's a paper out describing the representation of divalent ions,
>> particularly Zn+2, in the charmm force field. To guarantee accurrate
>> bond lengths, you'd have to do qm calculations, but depending on the
>> data you're hoping to generate, the charmm force field may be good
>> enough.
>> This is the paper:
>> R. H. Stote and M. Karplus. 1995. Zinc Binding in Proteins and
>> Solution: A Simple but Accurate Nonbonded Representation.
>> Proteins23:12-31.
>> Best of luck,
>> Meredith
>> On 8/2/06, Gaurav Sharma <> wrote:
>>> 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

Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
+49 30 450-528-446

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