From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 26 2011 - 10:53:05 CDT

Hi,
  It seems that psfgen doesn't like the X-PLOR format PSF file you've got,
although the VMD PSF plugin seems to read it without trouble.

Can you send me a gzipped copy of the PSF file that is causing you trouble?

This is most likely a limitation of the PSF reader currently in psfgen,
and is something we are looking at improving.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 22, 2011 at 11:03:30AM -0400, Edward Lyman wrote:
> 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
> get:
>
> 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.
> Ed

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078