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From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Jan 10 2011 - 13:22:26 CST

Dr. Olaf Lenz, author of pbctools, very kindly helped me solve my problem of wrapping protein units back into the water box in a Desmond trajectory.
 
Since PDB chain records were used, there are duplicate residue numbers in the various chains. Hence, atom index rather than resid is used to identify a center atom for the protein. The appropriate command is:
 
pbc wrap -all -center com -centersel "index 232" -compound res
 
-all means all frames.
-center com means center at the center of mass
-centersel selects atom 232 as the protein's center
-compound res means moving entire residues rather than individual atoms across the unit cell
 
I'm very grateful to Dr. Lenz for his help. I hope this example helps other users.
 
Irene Newhouse