From: Edward Lyman (
Date: Fri Apr 22 2011 - 10:03:30 CDT

Hi all,

I am trying to use psfgen to delete a couple of lipids and write a new
psf/pdb pair. The toplogy files read in fine, but when I read teh psf, I

reading structure from psf file 50_50_10nm.xplor.psf
Error processing bonds

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
psfplugin) Detected a Charmm31 PSF file
psfplugin) Detected a Charmm31 PSF EXTEnded file
Info) Using plugin psf for structure file 50_50_10nm.xplor.psf
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...

I am running vmd 1.9, psfgen 1.5. The psf file is an xplor psf (runs in
namd) that was written by the charmm gui. The psf/pdb pair work just fine
for reading into vmd.

Any help is appreciated.