VMD-L Mailing List

From: root (root_at_liposome.genebee.msu.su)
Date: Sat Dec 06 1997 - 08:08:16 CST

On Sat, 6 Dec 1997, Barry Isralewitz wrote:
[...]
> Could use a little more detail...what is VMD's response in the terminal
> window when you try to load the trajectory?

Dear Barry, thanks for your rapid response. I start vmd in the xterm
window. I select 'pdb and dcd' from the Mol->Load From Files menue, select
the proper 'Structure' and 'Coords' files, then press the 'Load Molecule'
button. The *.dcd file is not displayed in the Mol window:

TAD alanin.pdb: 000 66 1 File

is all I get. At that operation VMD quoth at the console:

[...]
Info) Reading commands from '/usr/local/lib/vmd/.vmdrc'.
Info) EOF encountered for current input file.
vmd >
Info) Loading new molecule ...
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 66 Bonds: 65
Info) Backbone bonds: Protein: 44 DNA: 0
Info) Residues: 12
Info) Waters: 0

Warning) Unusual bond between residues 1 and 2
Warning) Unusual bond between residues 11 and 12
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0

It doesn't seem to be reading in the *.dmd file. The Animate button nor
the animate forward command produce any response -- the helix just
continues floating.

What am I doing wrong?

Thank you,
Eugene