From: Axel Kohlmeyer (
Date: Fri Aug 01 2008 - 10:00:18 CDT

On Thu, 31 Jul 2008, Jianhui Tian wrote:

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


you have to use the proper -compound flag.


JT> Jianhui
JT> Biocomputation
JT> Rensselar Polytechnic Institute

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.