[gmx-users] Re: problem with Mn2+

[David van der Spoel]

On Thu, 2005-03-10 at 12:08 +0100, Ing. Vojtech Spiwok wrote:
> > Date: Wed, 9 Mar 2005 16:08:08 -0300
> > From: Maximiliano Figueroa <maxfigue at gmail.com>
> > Subject: Re: [gmx-users] problem with Mn2+
> > To: David <spoel at xray.bmc.uu.se>
> > Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <6297d4a105030911086bbd7027 at mail.gmail.com>
> > Content-Type: text/plain; charset=US-ASCII
> > 
> > I created Mn2+ in ffG43b1 and ffopls force fields. The parameters are
> > OK. With Hyperchem and Amber force field the problem is the same: the
> > Mn fly away from the active site. How I can simulated without lost the
> > Mn2+? (I have 2 Mn2+ in my active site)
> > 
> > Thanks
> > 
> 
> I would suggest using Buckingham potential fitted with literature
> or ab initio data. Advantage is that it is included in gromacs and
> V(r=infinity) = 0. Offcourse, protonation states are crictical.
You cannot combine Buckingham and LJ, and since there are no force
fields (in GROMACS) with Buckingham, this is not an option.
> 
> Vojtech Spiwok
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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