[gmx-users] Fe(II) at active site
X.Periole at rug.nl
Sat Jul 29 13:34:37 CEST 2006
> 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
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
The simulation that you discribe does not seem to be
a good representation of your system ...
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