[gmx-users] problem with Mn2+
mgoette at mpi-bpc.mpg.de
Thu Mar 10 11:40:31 CET 2005
I experienced exactly the same problems with Zn2+ ions.
If your Mn has to be flexible in movement, the bonded method should be
excluded. So there are two methods left (unbonded and cationic dummy
In that case you have to be aware of the complexing ligands and
especially their protonation state.
I would suggest to use it like:
Manzetti et al., Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in
complex with hypothetical substrates: New implications for catalysis and
substrate affinity J. Comp. Aid. Mol. Des. 17 pp. 551-565 (2003)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
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/
Maximiliano Figueroa wrote:
> 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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