From: Jacob Gissinger (
Date: Thu Jul 30 2015 - 16:01:23 CDT

Hello VMD,

The current -bondlist option of pbcjoin is unable to correctly join simple
chains such as the attached pdb because it does not actually walk the bond
list as claimed in the source code. Please find below an updated version of
pbcjoin.tcl which correctly joins large molecules.


Jacob Gissinger

Here is modified pbcjoin and example pdb. Wrap this and attempt to rejoin
to get full effect: