[gmx-users] Lennard-Jones parameters for manganese (Mn2+) ions

[Lieven Buts]

  Some time ago I asked about Lennard-Jones parameters for
divalent manganese ions. On the computational chemistry list
(http://www.ccl.net/), Marcel Swart suggested using the
parameters from the MM3 force field. These parameters are
(sigma,epsilon) or (s,e) pairs for the potential

  V(r) = 4*e*( (s/r)**12 - (s/r)**6 )

.

  Matching this with the potential as defined by GROMACS (

  V(r) = C12/(r**12) - C6/(r**6)

) I figure that C6 = 4*e*r**6 and C12 = 4*e*r**12 .

  To make the comparison I did the calculation for calcium
(using 1 cal = 4.1868 J and standard GROMACS MD units):
 
    MM3:  s = 2.77 angstrom = 0.277 nm
          e = 0.134 kcal/mol = 0.561 kJ/mol

    ---> C6 = 1.014e-3 kJ.(nm**6)/mol
        C12 = 4.579e-7 kJ.(nm**12)/mol

    ffgmxnb.itp: C6 = 0.10052E-02 = 1.0052e-3 ...
                C12 = 0.49800E-06 = 4.9800e-7 ...

    ffG43a1nb.ipt:             C6 = 1.00489e-3 ...
                              C12 = 4.9801e-7 ...


  Making the calculations for Mn2+ I get:

     MM3:  s = 2.20 angstrom = 0.22 nm
           e = 0.308 kcal/mol = 1.289 kJ/mol

     --->  C6 = 5.848e-4 kJ.nm**6/mol
          C12 = 6.631e-8 kJ.nm**12/mol


  Do these values seem reasonable?

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
http://ultr.vub.ac.be/~lieven