From: John Stone (
Date: Fri Apr 24 2009 - 08:03:21 CDT

  This error message is actually coming from psfgen. I'm currently out of
town serving on an advisory board, but I'll have a look when I return.

It seems that psfgen doesn't like something about the bond records
in that PSF file. It may be a minor limitation in psfgen's psf reader
that will require a code change, I'll let you know what I determine after
I return from travelling.

  John Stone

On Thu, Apr 23, 2009 at 11:41:07PM -0700, Gianluca Interlandi wrote:
> I am trying to solvate a protein using the solvate plugin of VMD. The PSF
> (X-PLOR format) and PDB were produced with CHARMM. I get the following
> error:
> vmd > solvate protein_xplor.psf protein.pdb -minmax {{-65 -65 -65} {65 65
> 65}}
> reading structure from psf file protein_xplor.psf
> Error processing bonds
> I'm using vmd version 1.8.6 on linux.
> I have uploaded the files here:
> Any help would be appreciated.
> Gianluca

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