From: Dongsheng Zhang (zhdsheng21_at_yahoo.com)
Date: Thu Jan 17 2008 - 16:23:27 CST

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

      ____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping