Hi,
This does seem like strange behavior. Can you provide some more
information so we can figure out what might be going on? What version
of AmberTools were you using (1.5?), what bugfixes are applied, which
program did you use (tleap, sleap, or xleap), and what input did you
give it? Also, could you attach the coords/topology that leap
generated? Thanks!
-Dan
On Fri, Jul 22, 2011 at 1:22 AM, Wei Chen <cwbluesky.gmail.com> wrote:
> Hi, All,
>
> After I solvated my protein, I used "addIons" to add ions to the
> system to reach certain ion concentration. I found that some ions were
> placed outside of the water box. Is this normal? When I used AMBER8
> long time ago, this did not happen. I was wondering if this is
> something with the new version of AmberTools.
>
> Thanks!
>
> Wei Chen
>
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Received on Fri Jul 22 2011 - 04:30:05 PDT
