Re: coordination chemistry with NAMD

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Wed Aug 02 2006 - 14:40:55 CDT

Gaurav,
   I am not sure about Charmm but you can do that in amber ff. You can
create a bond between the Zn and the nitrogens using the 'bond'
command and then use the parameters in Ross walker's thesis available
on his website.

Nitin
On 02/08/06, Gaurav Sharma <sharma_at_coe.neu.edu> 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
>
>
>

-- 
$B&-(BI+I$B'*(B

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