On Thu, May 5, 2016 at 9:45 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to calculate the LJ parameters, atomic radius and well depth,
> for a divalent metal ion from the A coefficient and B coefficient provided
> in the literature. The A and B coefficient for the ion are follows,
>
> A = 171.0 , B = 35.0
>
> Following the methodology described in
> http://ambermd.org/Questions/vdw.html
> , the calculated values of radius and well depth are, 0.8274 Angstroms and
> 12.8298 kcal/mol respectively. Looking at the Amber parameters for ions,
> the calculated values look quite odd to me as with the a relatively small
> radius and a very high well-depth potential. I just wonder if there is any
> alternate way to calculate the radius and well depth with the provided the
> A and B coefficients.
>
No.
> Many thanks in advance
>
ParmEd does this calculation. A- and B-coefficients are *pairwise*
coefficients -- they are calculated for each pair of atom types. So a
single atom type doesn't have an A- or B-coefficient. What ParmEd does is
to look at the pairs of each atom type with itself, then back-calculates
the Rmin and epsilon parameters from there. That's the easiest way to do
it, since for each atom type you get two equations (the A- and
B-coefficients expressed as a function of the sigma and epsilon parameters)
and two unknowns (sigma and epsilon).
You can see the code that does that here:
https://github.com/ParmEd/ParmEd/blob/master/parmed/amber/_amberparm.py#L777-L807
HTH,
Jason
--
Jason M. Swails
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Received on Thu May 05 2016 - 07:30:04 PDT
