[gmx-users] manganese parameters in Gromacs

T.A.Wassenaar T.A.Wassenaar at rug.nl
Wed Jun 22 14:45:21 CEST 2005

Hi Luciane,

The parameters for a Mn-containing center are pretty much 
dependent on the surroundings. So if you're only desire is 
to keep te stuff together, then you can add something not 
too unreasonable for the bonds and angles (from the 
structure file maybe). If the behaviour of the center is 
an important part of your study, you'll have to do the 
calculations with a model for the coordinating residues 
specific to your protein.

Hope it helps,


On Wed, 22 Jun 2005 09:00:26 -0300 (BRST)
  "Luciane V.  Mello " <mello at cenargen.embrapa.br> wrote:
> Dear all,
> I'd like to do a simulation in Gromacs of a protein 
>bound to two
> manganese ions.
> Would you have a modified topology and parameter files 
>which you would
> consider sharing with me, to save me the trouble of 
>redoing the
> calculations? 
> Many thanks in advance
> Luciane
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