I'd be wary of those specific parameters, especially if there's going to be
a charge on the Pt. With no Lennard-Jones properties it would be like a
polar hydrogen, possibly with a very large charge, and significantly more
spacing between it and any ligands with steric properties to help shield it
from bad interactions (i.e. water oxygen comes in and becomes
electrostatically attracted to the bare Pt core).
You might try putting some nominal Lennard-Jones parameters on the Pt, and
making use of Pengei Lee's MCPB.py tool (metal center parameter builder).
It implements the Seminario method, in particular, for deriving bonded
parameters to and from a metal center with the Hessian from a DFT
calculation. That may get you reasonable parameters for a totally bonded
model, and a fully bonded model would allow you to carry significant LJ
parameters on the Pt without disrupting the surrounding ligands (the LJ
interactions between Pt and bonded ligand atoms would be omitted by 1:2
exclustions).
When you assign LJ parameters to metal ions, don't fall into the trap that
some have before: using a very small Lennard-Jones epsilon. What this does
is push back the point at which any significant repulsive force is felt,
until WHOOSH the r12 potential kicks in big time. It creates a "hard wall"
sort of effect that will hurt your energy conservation with standard MD
integrators. Rather like the computational equivalent of shaking a ketchup
bottle until you finally exceed the shear needed to thin the fluid and dump
it all over your plate. Use epsilons in the range 0.1 to 0.25 kcal/mol if
at all feasible.
Dave
On Wed, Jun 29, 2016 at 4:34 AM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Wed Jun 29 2016 - 02:30:03 PDT
