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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Received on Fri Jul 02 2010 - 08:00:03 PDT
