[gmx-users] Modeling Zinc in OPLS

[Maik Goette]

Hi

I also use Zn in my simulations.
There are 3 possibilities:
Bonded, nonbonded and cationic dummy atom approach.
Unfortunatly, nothing except the bonded approach worked for me.
If you need help with the bonded approach, tell me.
If you are able to work with one of the both nonbonded methods, tell me.
What is the job of zinc in your sim?

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Sandeep Somani wrote:
> Hi 
> 
> I have a Zn atom in my protein cordinating with CYS and HIS. 
> 
> Is it fine to model it with just the non-covalent interactions (using
> parameters available in the OPLS force filed) or a bonded interaction
> should be considered ?  
> 
> Thnx & Rgds
> Sandeep 
> 
> ---
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> Computational Biology Group
> Bioinformatics Institute 
> Singapore
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