The parameters there are the Lennard-Jones sigma divided by 2^0.83333, in
other words times sigma times 2^(1/6) and divided by 2, followed by the
Lennard-Jones epsilon. These are natural quantities to consider, as twice
the first number will give the location of the minimum, and the second
number will give the depth of the minimum. It's also numerically more
convenient to work with those two quantities rather than the raw sigma and
epsilon if you write out the formula and factorize it (for similar reasons,
the partial charges in Amber topology files are scaled by 18.2223, the
square root of the famous conversion factor of 332.0535).
It looks like platinum in your frcmod, and yes, I can see how someone would
write in the comment "ATTN, needs revision." I don't think anyone has
decent Lennard-Jones parameters for platinum, and I doubt a general-purpose
pair of numbers truly exists.
Dave
On Wed, Jun 29, 2016 at 12:26 AM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> Dear Amber users,
> I wonder what's the meaning of values in NONBON section of frcmod, e.g.
> NONBON
> Pt 0.0000 0.0000 ATTN, need revision
> I check the website and the two values may be type RE(van der Waals radius
> and the potential well depth parameters) or AC(The 6-12 potential
> coefficients), so how could I know which type these two values stand for?
> Your kind help will be highly appreciated!
>
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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>
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Received on Tue Jun 28 2016 - 22:00:02 PDT
