VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Jun 24 2006 - 22:51:13 CDT

yOn Sat, 24 Jun 2006, Xu wrote:

FX> Hello,
FX> I want to visualize a polymer chain described by a set of bead-rod. In
FX> order to introduce the bond information, I wrote a fake psf file as
FX> following:

FX> 10 !NBOND: bonds
FX> 1 2 2 3 3 4 4 5
FX> 5 6 6 7 7 8 8 9
FX> 9 10 10 11

the error is here. the numbers have tobe 8-spaced but right aligned
with a step of 8, so if you delete a blank after the 9 it should work:

FX> 9 10 10 11

cheers,
    axel

FX> However, VMD can not read the bond information and gives the error
FX> information:
FX>
FX> ERROR) Error reading bond information.
FX> Info) Analyzing structure ...
FX> Info) Atoms: 11
FX> Info) Bonds: 0
FX> Info) Residues: 11
FX> Info) Waters: 0
FX> Info) Segments: 2
FX> Info) Fragments: 11 Protein: 0 Nucleic: 0
FX>
FX> Why is that? Is there any constraint on defining bonds? Any suggestions?
FX> Many thanks.
FX>
FX> Fang
FX>
FX>
FX> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.