[gmx-users] Fe(II) at active site

raja raja_28 at fastmail.us
Sat Jul 29 14:17:34 CEST 2006

Hi XAvier,
Thanks for your opinion. This is my maiden attempt to simulate a protein
so the reason for the mistake. If possible could you please refer me
some paper, which describe the simulation of a system, contains Fe (II)
at its active site. I tried my best, but could not find a one.


On Sat, 29 Jul 2006 13:34:37 +0200, "X.Periole" <X.Periole at rug.nl> said:
> > During the simulation of protein with Fe (II) ligating 
> >with 2 His and 1
> > Asp residues at active site, I set every thing right 
> >including Kb value
> > but failed to deprotonate NE2 atoms of 2 His residues 
> >ligating that
> >Fe(II). 
> What do you mean by failed ? This should not be a problem.
> You can choose the protonation state of a his ... check
> the ffXXX.rtp file.
> > After 2ns simulation run, the average pdb 
> >structure shows that
> > the flip of His ring out from Fe (II), but the 
> >Asp-oxygen moved much
> > closer to Fe (II) than its original position. If I 
> >compute RMSF for Fe
> > (II), showing value of "0" through out the simulation 
> >run.  The RMSF "0"
> > indicates Fe (II) originally retained in its position, 
> 0 fluctuations at all !!! You fixed its position or
> something ? That does not seems right !!
> >but the ligating
> > His flipped and Asp as a single residue held the Fe (II) 
> >at its original
> > position. So now please tell me whether this simulation 
> >is valid?
> The simulation that you discribe does not seem to be
> a good representation of your system ...
> XAvier
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  raja_28 at fastmail.us

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