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From: Jason Swails <jason.swails.gmail.com>

Date: Thu, 5 May 2016 10:08:38 -0400

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

Date: Thu, 5 May 2016 10:08:38 -0400

On Thu, May 5, 2016 at 9:45 AM, anu chandra <anu80125.gmail.com> wrote:

No.

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu May 05 2016 - 07:30:04 PDT

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