VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 24 2009 - 08:03:21 CDT

Hi,
  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.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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:
>
> http://artemide.bioeng.washington.edu/Files/protein_xplor.psf
>
> http://artemide.bioeng.washington.edu/Files/protein.pdb
>
>
> Any help would be appreciated.
>
> Gianluca 

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