From: Jim Pfaendtner (
Date: Thu Jul 10 2008 - 08:56:32 CDT

Dear vmd-l,

I am trying to build a bicyclic polypeptide using psfgen and vmd. The
first ring is created by joining the first and last residues with
patch LINK, and this works without difficulty. The second ring is
created because there is a nonstandard bond between two CYS and TRP
residues as in phalloidin. The S atom in CYS bonds as if it was in a
disulphide bridge, but it bonds with the CD1 atom of TRP.

I have not found a straightforward way to do this with the patch
command. Does anyone have any suggestions? Of course, one option is
to simply put a harmonic bond between the two atoms, but this is quite
coarse and not preferred. I would also like to avoid trying to
manually change the psf.

Thank you,