From: Hendrik Schröder (
Date: Tue Apr 07 2020 - 13:17:07 CDT

Hi VMD and NAMD users

I try to build a psf file for a peptide with linkage between its N-terminus
and a side chain (=isopeptide bond, =cyclic-branched peptide). Psfgen does
not recognize this extra bond and creates a linear version of a peptide
(see for example PDB: 1PP5). After reading forum threads on cyclic
peptides and checking manual/tutorials, it seems like a very common problem
without solution yet.

I would be very happy if someone could point out a strategy (preferably for
beginners) to convert a pdb of a peptide with side chain linkage into a
psf-file. Maybe someone has a suitable topology file already and could send
it to me.

Thank you so much and with my best wishes,