AMBER Archive (2003)

Subject: Re: Distribution Min with truncated octahedron box

From: Bill Ross (photoriot_at_yahoo.com)
Date: Tue Jul 08 2003 - 13:24:09 CDT

> I want to select the waters around the solute
> using INH2O with Distribution Min in Amber6.
> The problem is that I used the truncated
> octahedron box. I wandered whether the
> calculation will be wrong because of the
> box shape?

The 'original' truncated octahedral box is handled
by carnal (amber7 and I suspect amber6). The 'ewald
truncated octahedral box' is not - amber7 carnal
prints a warning about this situation, to check
amber6, cd to src/carnal and 'grep -i oct *.c' to
see if there's a message in util.c. I'm not sure
which version of the box you'd be using, if it's
the ewald one, some programming would be required
to adapt carnal for it.

Bill Ross