VMD-L Mailing List

From: James Rustad (rustad_at_geology.ucdavis.edu)
Date: Mon Jan 16 2006 - 22:27:30 CST

John,

To be more specific from an earlier post:
I use the following command to load the trajectories:

vmd> for {set i 1} {$i < 2501} {incr i} {mol new [format "%04d.xyz"
$i] }

then I get:
.........

Info) Using plugin xyz for structure file 0243.xyz
Info) Using plugin xyz for coordinates from file 0243.xyz
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 32
Info) Residues: 12
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 12 Protein: 0 Nucleic: 0
ERROR) Could not read file 0244.xyz

but if I then type

vmd > for {set i 244} {$i < 2501} {incr i} {mol new [format "%
04d.xyz" $i] }:

Info) Using plugin xyz for structure file 0244.xyz
Info) Using plugin xyz for coordinates from file 0244.xyz
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 31
Info) Residues: 13
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 13 Protein: 0 Nucleic: 0

...........

Info) Using plugin xyz for structure file 0486.xyz
Info) Using plugin xyz for coordinates from file 0486.xyz
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 33
Info) Residues: 13
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 13 Protein: 0 Nucleic: 0
ERROR) Could not read file 0487.xyz

So I can go on loading molecules in chunks like this,
but the commands I gave don't allow everything to be loaded at once.

It seems very odd to me. I am new to TCL; did I make a boneheaded
mistake?

This is on a G4 laptop running tiger and VMD 1.8.3

But I seem to recall I had the same problem about a year ago, with
older OS and VMD

Thanks for any help

(great code, by the way!)

Jim Rustad