[gmx-users] parameters for Mn2+

lieven at ultr.vub.ac.be lieven at ultr.vub.ac.be
Tue Jul 25 15:20:46 CEST 2006

This is the message I originally posted in 2002:

  I have been looking again at the Lennard-Jones
parameters (C6 and C12) I tried to derive from
the MM3 force field epsilon and sigma values for
manganese (Mn2+). 

  First of all, I compared the MM3-derived values
for calcium (C6=1.014e-3 kJ.nm**6/mol; C12=4.579e-7
kJ.nm**12/mol) with the values defined in
ffgmxnb.itp (C6=0.10052E-02; C12=0.49800E-06).
The potential functions are plotted in red (MM3-
derived) and green (ffgmxnb.itp). The curves are
very similar. The minimum energy is slightly higher
for the MM3-derived values.
  The blue curve is the potential for the values
I calculated for manganese from the MM3 values
(C6=5.848e-4; C12=6.631e-8).

  Next, I calculated the positions of the energy
minima (sixth root of (2*C12)/C6):
                                 r_min (nm)
        calcium, ffgmxnb.itp        0.316
        calcium, MM3-derived        0.311
        manganese, MM3-derived      0.247

  I then tried to compare this with published
van der Waals and ionic radii, but so far this 
is very confusing. The ionic radius for Mn2+
in an octahedral coordination is 0.110 nm. 
The corresponding value for Ca2+ is 0.126 nm.

  Now I will check if the manganese binding site
maintains the correct geometry during a dynamics
run with these parameters.

The stability of the coordination turned out to be OK. I 
never got round to my complete in-depth study of sugar 
binding by this metalloprotein, though :-) .

Lieven Buts
Department of Ultrastructure

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