[gmx-users] Zinc-coordinated protein simulation

[Sandeep Somani]

For Zn parameters you may also refer to 

"Zn protein simulations including charge transfer and local polarization
effects"
J Am Chem Soc. 2005 Apr 6;127(13):4921-9.
Sakharov DV, Lim C.

-sandeep


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Maik Goette
> Sent: Friday, August 19, 2005 9:02 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Zinc-coordinated protein simulation
> 
> 
> The method, David mentioned is a third possibility.
> It depends, what goal you want to achieve.
> If the Zinc is complexed and "just" important to stabilize 
> your structure, the bonded method also works. The problem 
> with that method is, that, as I know, no parameters are 
> available. I took the mean of the distances in the crystal 
> structure as bond length and a weak force constant, which I 
> took by intuition...:). I did the same for the angles. I 
> think, you don't have to care about the dihedrals...It worked 
> fine with no settings (so GROMACS sets 0s, when I remember 
> correctly). The charge on the zinc shouldn't be 2, according 
> to severeal papers, which used that method. with a charge of 
> around .7 it worked fine. Don't forget to spread the opposing 
> charges equally to the 4 complexing atoms, to achieve a 0 
> total charge. If your zinc has a catalytical function, you 
> should try the dummy method. This never worked for me, but as 
> I now know, I made fatal mistakes in configuring it. So just 
> give it a try...I will do that in the future again, but at 
> the moment, this has no priority.
> 
> 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/
> 
> 
> Linda wrote:
> > Dear gmx user,
> > 
> >     I just searched gmx mailing list about the 
> zinc-coordinated enzyme 
> > simulation, it seems that most people encouter the problem that the 
> > zinc goes away from coordinated residue (Cys/His) in enzyme. I saw 
> > some people tried to solve this problem with two methods: 
> 1. cationic 
> > dummy atom method. 2. bonded zinc with His or Cys. I wonder someone 
> > has succeeded? If so, would you please share your 
> experience? Thanks.
> > 
> > Cheers,
> > 
> > Linda
> > 
> > 
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