From: JC Gumbart (
Date: Mon Feb 23 2009 - 00:55:11 CST

Are you sure the appropriate psf and dcd are loaded in vmd when you source
the script? I just tested it on the example output and it worked for me.

The semicolon doesn't matter. Also, it won't work from the terminal because
it's a tcl script, meant to be used only in VMD.

-----Original Message-----
From: [] On
Behalf Of Corey Fugate
Sent: Thursday, February 19, 2009 1:41 PM
Subject: tutorial-l: empty rmsd.dat file

        I am working through the NAMD tutorial on my mac 10.5. I am stuck
section 1.7.1. When I run source rmsd.tcl through the TkCon window
the is nothing printed to the TkCon and the rmsd.dat that is punched
is blank. I tried running source rmsd.tcl from terminal (while in the
1-2-sphere directory) and I receive the following message.

-bash: rmsd.tcl: line 7: syntax error near unexpected token `i'
-bash: rmsd.tcl: line 7: `for {set i 1 } { $i < $nf } { incr i } {'

I looked at the rmsd.tcl file included in the tutorial and noticed
that line 1 ends with a semicolon and the source described in the
tutorial does not. Removing the semicolon has not effect.

                                Any help would be great,

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