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

[raja]

Hi all,
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). 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, 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?

More all-globular validation of the entire simulation is perfect.

Kindly give me yours valid opinion.

With thanks!
B.Nataraj
-- 
  raja
  raja_28 at fastmail.us

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