# Re: [AMBER] Calculating LJ parameters in Amber format

From: anu chandra <anu80125.gmail.com>
Date: Thu, 5 May 2016 16:15:52 +0100

Dear Jason and Prof. Case,

Many thanks for correcting me. Here, I am trying to develop a dummy atom
model for different divalent metal ions using the parameters mentioned in
the article, http://pubs.acs.org/doi/abs/10.1021/jp501737x . Please do
correct me if I am doing anything wrong with translating the parameters
here.

Many thanks
Anu

On Thu, May 5, 2016 at 3:28 PM, David A Case <david.case.rutgers.edu> wrote:

> On Thu, May 05, 2016, anu chandra wrote:
> >
> > 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.
>
> First, I wonder if you are interpreting the web page correctly? Assuming
> that
> the above parameters have their usual meanings, the minimum distance r*
> is (2A/B)^1/6 = 1.462 (remember that Amber uses rmin = r*/2 in its
> parameter
> files) and eps = B^2/4A = 1.79 kcal/mol.
>
> *More importantly*: you must be *very* careful in translating ion
> parameters
> from the literature!. Be sure that the units are in kcal/mol and not
> kJ/mol.
> Be aware that the mixing rules common in the literature may be different
> than
> those Amber uses (remember that your ions will most commonly be interacting
> with water molecules, not with other ions.) Ion parameters are very
> sensitive
> to which water model is being chosen.
>
> Amber parameters are available for dozens of divalent ions, and have been
> optimized for various water models. Please review carefully the
> information
> in the "Ions" section of the Amber Reference Manual, and consult the papers
> referred to there.
>
> ....good luck....dac
>
>
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Received on Thu May 05 2016 - 08:30:03 PDT
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