[AMBER] Calculating LJ parameters in Amber format

From: anu chandra <anu80125.gmail.com>
Date: Thu, 5 May 2016 14:45:58 +0100

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.

Many thanks in advance

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Received on Thu May 05 2016 - 07:00:03 PDT
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