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
>>
>
>
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Received on Wed Jun 29 2016 - 02:30:04 PDT
