[gmx-users] problem with Mn2+
maxfigue at gmail.com
Wed Mar 9 20:08:08 CET 2005
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)
On Wed, 09 Mar 2005 19:35:12 +0100, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-03-09 at 14:35 -0300, Maximiliano Figueroa wrote:
> > Dear Gromacs users:
> > We are working with a protein that include
> > Mn2+ in the active site, using the parameter presented here some time ago, we
> > were able to run some MD, but the Mn2+ fly away from the active site.
> > We try distance restraints but we received a error
> > Fatal error: [ file "mutanteSI.top", line 18748 ]:
> > Atom index (1118) in distance_restraints out of bounds (1-1) ??
> > Any hint to keep the Mn2+ in the active site will be relly very appreciate!!
> Mn2+ has to be part of the protein to be able to use distance
> restraints. Are you sure force field is correct and ligation is not
> > Two crazy boy
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> 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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