From: Peter Freddolino (
Date: Fri Aug 01 2008 - 10:14:47 CDT

Hi Jianhui,
try using the -compound option to enforce wrapping groups together (see
the manual page for the possible options; generally -compound res works
well if you're just worried about broken waters, -compound chain otherwise).

Jianhui Tian wrote:
> Hi,
> I used pbctools to wrap my system for better visualization. The
> command I used is {pbc wrap -center "resid 1" -all}. After all is
> finished, I see broken molecules, which means the whole molecule is on
> the edge of the new box, half of the molecule is on one side and half
> on the other side and wired bond connecting them. How can I avoid
> such broken molecules?
> Jianhui
> Biocomputation
> Rensselar Polytechnic Institute