VMD-L Mailing List

From: Xu (fangxu_at_levdec.engr.ccny.cuny.edu)
Date: Sat Jun 24 2006 - 20:51:27 CDT

Hello,
I want to visualize a polymer chain described by a set of bead-rod. In
order to introduce the bond information, I wrote a fake psf file as
following:
PSF
    11 !NATOM
       1 U 1 0 C C 0.00000 0 0
       2 U 1 0 C C 0.00000 0 0
       3 U 1 0 C C 0.00000 0 0
       4 U 1 0 C C 0.00000 0 0
       5 U 1 0 C C 0.00000 0 0
       6 U 1 0 C C 0.00000 0 0
       7 U 1 0 C C 0.00000 0 0
       8 U 1 0 C C 0.000000 0 0
       9 U 1 0 C C 0.00000 0 0
       10 U 1 0 C C 0.00000 0 0
       11 U 1 0 C C 0.00000 0 0

    10 !NBOND: bonds
       1 2 2 3 3 4 4 5
       5 6 6 7 7 8 8 9
       9 10 10 11
However, VMD can not read the bond information and gives the error
information:

ERROR) Error reading bond information.
Info) Analyzing structure ...
Info) Atoms: 11
Info) Bonds: 0
Info) Residues: 11
Info) Waters: 0
Info) Segments: 2
Info) Fragments: 11 Protein: 0 Nucleic: 0

Why is that? Is there any constraint on defining bonds? Any suggestions?
Many thanks.

Fang