Dear David,
Thanks for your information.
I'm now working with a Pt complex interacting with DNA, I planed to
constrain the distance between Pt and ligand atoms because as you said, no
existing ff parameters for Pt.
I also refer to UFF(universal force field) and in it there are LJ
parameters for Pt, I wonder is that OK to use only the LJ parameters in UFF
for Pt and GAFF for the rest of my complex?
2016-06-29 12:44 GMT+08:00 David Cerutti <dscerutti.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Wed Jun 29 2016 - 02:00:02 PDT
