From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 20 2008 - 20:46:28 CST

Hi,
  My guess is that the conversion script you used generated a
non-conformant PSF file that doesn't strictly follow the columns
required for proper parsing. If you can gzip up one such PSF file
and email it to me I would be happy to take a look, but it may be best
to contact the author of the conversion script and get them involved
as well, since this is almost certainly a bug in their conversion
script.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 17, 2008 at 02:23:27PM -0800, Dongsheng Zhang wrote:
> Hello, vmd and lammps users:
>
> I have a pdb and psf file generated from lammps data file by lammps2pdb.pl script. When I loaded vmd, vmd complained the psf file as:
>
> Error reading optional structure information from coordinate file gel_trj.psf Will ignore structure information in this file.
>
>
>
>
> Part of the psf file is:
>
> PSF
>
> 2 !NTITLE
> REMARK gel_trj.psf GENERATED FROM gel.data
> REMARK CREATED BY lammps2pdb v2.2.5 ON Thu Jan 17 16:10:01 CST 2008
>
> 0 !NATOM
>
> 3120 !NBOND
> 1 2 1 41 2 3 2 42
> 3 4 3 43 4 5 4 44
> 5 6 5 45 6 7 6 46
> 7 8 7 47 8 9 8 48
> 9 10 9 49 10 11 10 50
> 11 12 11 51 12 13 12 52
> 13 14 13 53 14 15 14 54
> ....
> 1596 1597 1597 1598 1598 1599 1599 1600
>
>
> In the pdb file, the total number of atoms is 2080. The number of all connected atoms is 1600. The rest are free atoms around. I don't know why NATOM is zero in the psf file. If I change it to 1600, I got the same error. If I changed it to 2080. I got another error:
>
> Line too short in psf file:
> couldn't read atom 0
>
>
> Could someone tell me what's wrong with the psf file? Thanks!
>
> Dongsheng
>
>
>
>
>
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-- 
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