You should never copy parameters from other works or ff except there is
great similarity in MD with your work.
MCPB.py is an excellent Ambertool for the metal containing macromolecules,
just follow tutorial from Amber pages (take care particularly on QM part)
and everything will be just fine with your modeling and simulation work. In
my opinion it is much better than majority of other semi-automatic programs
made for the same purpose (checked by myself).
Cheers
Zoran
Dear David,
Thanks for your suggestions, that would be very helpful!
Just now I read some the UFF related papers and it seems the LJ form for
that FF has an extra parameter, so it cannot be employed in amber directly,
I think.
I'll first try to use MCPB.
2016-06-29 17:11 GMT+08:00 David Cerutti <dscerutti.gmail.com>:
> Oops... edit... be wary of "0.0 and 0.0" for Pt parameters. I don't know
> specifically what UFF has.
>
> On Wed, Jun 29, 2016 at 5:11 AM, David Cerutti <dscerutti.gmail.com>
> wrote:
>
> > 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
> >>
> >
> >
> _______________________________________________
> AMBER mailing list
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> 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
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Received on Wed Jun 29 2016 - 04:30:03 PDT
