If your values are too small then molecules with lots of branches could get
tangled up. But anything that comes out of AddToBox will need energy
minimization.
On Tue, Jan 8, 2019, 6:59 AM Lucas Bandeira <bandeiralucas97.gmail.com>
wrote:
> Thank you very much.
>
> But if I use smaller values, it cause some problems with the properties of
> the system. For instance, I have used RP 2.0 and RW 2.0, could this values
> mislead over the values of energy calculated?
>
> Thank you
>
> Lucas
>
> On Tue, Jan 8, 2019 at 12:27 PM David Cerutti <dscerutti.gmail.com> wrote:
>
> > There are defaults for those values. Generally you want RP to not go
> below
> > 2 or 2.5. The solvent:solvent clipping radius can be very high for
> adding
> > small numbers of rare species, so make sure they are spread out. The
> > clipping radius is the minimum distance that AddToBox will allow any
> atoms
> > of a new molecule to be placed from existing protein or solvent atoms.
> The
> > "protein" atoms are defined as the first -P atoms of the system,
> everything
> > else is solvent. Add rare, large species of solvent first, then smaller
> > and more common ones.
> >
> > Dave
> >
> >
> > On Tue, Jan 8, 2019 at 9:07 AM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Tue, Jan 08, 2019, Lucas Bandeira wrote:
> > > >
> > > >Could one help me with the term "clipping radius". What it exactly
> means
> > > >and how can I find the right values for protein atoms and for solvent
> > > atoms
> > > >( -RP and -RW in AddToBox).
> > >
> > > This is not definitive, but I always use RP of 2.5 and RW of 2.8 for
> > > either waters or monatomic ions. I remember that years ago I played
> > > around with these values (and you can experiment as well), but I don't
> > > seem to be able to find the record of how I arrived at these values....
> > >
> > > If you are adding bigger solvent molecules, you will probably have to
> > > experiment some: see the Reference manual for suggestions.
> > >
> > > [Dave: should we not add some defaults, and suggested values (maybe
> > > different than those above) to the Manual?]
> > >
> > > ....dac
> > >
> > >
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Received on Tue Jan 08 2019 - 07:30:02 PST
