PSF for Cyclic-Branched Peptides

From: Hendrik Schröder (
Date: Sun Apr 05 2020 - 17:20:18 CDT

Hi NAMD community,

I am a beginner having troubles to convert a pdb- to a psf-file for
cyclic-branched peptides, a structure in which an N-terminus is linked to a
Glu or Asp side chain in the middle of the sequence (see PDB code 1PP5).
Psfgen does not recognize this extra bond and always creates the linear
version of the peptide. I read the forum threads on cyclic peptides, read
the manual sections on patches and I checked the “topology file tutorial”,
but my attempts to create a new topology file failed.

I would be very happy if someone could point out a strategy or a way
(preferably for beginners) to convert a pdb of a cyclic-branched peptide
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,


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