Re: PSF for Cyclic-Branched Peptides

From: Aravinda Munasinghe (
Date: Sun Apr 05 2020 - 19:46:40 CDT

I assume you are doing this using VMD psfgen (in which case you are mailing
the wrong thread). In any case, I think what you are doing wrong is not
defining a patch between two residues forming the cycling bond. And make
sure you say first none and last none to avoid two ends being capped (if
the first and last are the two residues creating the loop).

Aravinda Munasinghe
PhD Candidate |*|* Colina Research Group
George and Josephine Butler Polymer Research Laboratory
Center for Macromolecular Science and Engineering
Department of Chemistry |*|* University of Florida
Vice President of Mayors' Council

On Sun, Apr 5, 2020 at 6:58 PM Hendrik Schröder <> wrote:

> 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,
> Hendrik

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