I would recommend:
Empirical force fields for biologically active divalent metal cations in
water.
C Satheesan Babu, Carmay Lim (2006)
*The journal of physical chemistry. A* 110 (2) p. 691-9
http://dx.doi.org/10.1021/jp054177x
they calculated and tested the LJ parameters of 26 divalent metal cations.
Maybe you can find it useful.
Best,
Rodrigo
2011/11/13 case <case.biomaps.rutgers.edu>
> On Sun, Nov 13, 2011, Dr. Vitaly V. Chaban wrote:
> >
> > Does the AMBER force field contain LJ-12,6 parameters for calcium? I
> > can find parameters for Mg, Zn, etc, yet not for calcium. What is the
> > name for this atom type?
>
> We have old parameters in parm10.dat: look for atom type "C0", and the
> literature reference there. You would have to create a unit for this: see
> $AMBERHOME/dat/leap/lib/ions08.cmd for sample input commands to LEaP that
> would do this.
>
> It should be pretty clear that these are not "supported" Amber parameters;
> generally, simple fixed charge plus LJ parameters have lots of problems for
> divalent ions. So, treat these with care.
>
> ....dac
>
>
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Received on Sun Nov 13 2011 - 20:00:02 PST
