Great, as mentioned previously, though, you can also use tleap, then run the
resulting restart file through ptraj and use randomizeions, as described in
the ambertools manual. I think using sleap is probably the best option
though, since it will hopefully replace tleap someday (and it's actively
developed).
All the best,
Jason
On Fri, Jul 2, 2010 at 10:45 AM, Ajay Ummat <ajayummat.gmail.com> wrote:
> The sleap did work for adding ions for my system, but with installing all
> the latest bug fixes for it. Adding these ions individually in tleap doesnt
> work as it still places the ions on a particular side of the protein. But
> anyhow the latest fix on sleap helps!
>
> Thanks everyone.
>
> Aj
>
> On Wed, Jun 30, 2010 at 2:15 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Wed, Jun 30, 2010, Ajay Ummat wrote:
> >
> > > I want to add 150mM Na+ Cl- ions in my system. I used the command:
> > addions x
> > > Na+ 91 Cl- 96 (as my system had +ve 5 charge and I needed 96 each of
> Na+
> > and
> > > Cl-). When I visualize the result of adding ions, leap has added all
> the
> > > ions only on one particular side of the protein.
> >
> > This sounds like an old problem...what version of AmberTools are you
> using?
> >
> > One thing you might try is to use sleap rather than tleap, to see if that
> > helps.
> >
> > ....dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jul 02 2010 - 09:30:03 PDT
