[gmx-users] Modeling Zinc in OPLS
ssomani at bii.a-star.edu.sg
Wed Mar 2 10:58:29 CET 2005
In my protein the Zn is bonded to 3 CYS and a HIS and is stabilising the
So ill also have to use the bonded approach which means there will be
change in parameters for the surrounding CYS and HIS too (?).
waiting for more details from you ..
thnx & rgds
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Maik Goette
> Sent: Wednesday, March 02, 2005 4:43 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Modeling Zinc in OPLS
> 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?
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.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
> > should be considered ?
> > Thnx & Rgds
> > Sandeep
> > ---
> > Research Associate
> > Computational Biology Group
> > Bioinformatics Institute
> > Singapore
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