Dear Zoran,
Thanks for your suggestion, I'll try MCPB first.
2016-06-29 19:12 GMT+08:00 zoran matovic <zmatovic.kg.ac.rs>:
> 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
> > 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
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>
>
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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 Thu Jun 30 2016 - 05:30:02 PDT
