Re: Error Running ubq-get-energy.conf

From: Jim Phillips (
Date: Wed Oct 22 2003 - 18:50:49 CDT


You must use NAMD 2.5 (actually 2.5b2 or later) for this example. This
(stunningly useless) error message is generated by 2.5b1 or earlier.

What is actually happening is that since "coorfile" isn't recognized as a
valid Tcl command it is passed to Tcl's "unknown" command, which has been
redefined to parse its arguments ("coorfile read") as a NAMD config
option. NAMD tries to read in all of its config options until the end of
the file or an action command like "run" or "coorfile", and prints a list
of any unrecognized options at that point (and continued without them in
2.5b1 and earlier, which wasn't very nice).

In any case, this "unknown" command doesn't return anything or raise and
error, which makes "![coorfile read]" the same as the non-sensical "!{}",
and sure enough if you try to use this in Tcl you get:

% expr { !{} }
can't use empty string as operand of "!"

Since "coorfile read" is currently the only NAMD command that returns an
error code like this, this is the first case of this error I've seen.


On Thu, 16 Oct 2003, Raymond C. Fort Jr. wrote:

> I'm still working through the namd tutorial from the web site. While
> attempting to run the ubq-get-energy.conf simulation, I get the following
> error message:
> [rcfort_at_pemetic 2-5-spec_heat]$ Fatal error on PE 0> FATAL ERROR: can't use
> empty string as operand of "!"
> while executing
> "while { ![coorfile read] } {
> incr i 50 ;#since the dcd was saved every 50 steps in the ubq-nvt
> simulation
> firsttimestep $i
> run 0
> }"
> (file "ubq-get-energy.conf" line
> 155)
> The ubq-nvt-prot.dcd file is definitely present, all 88 MB of it.
> Any suggestions?
> Ray
> Professor Ray Fort Jr. Voice: (207)-581-1180
> Department of Chemistry FAX: (207)-581-1191
> University of Maine EMail:
> Orono, ME 04469 Web:
> Molecular modeling of organic and biological molecules; chemistry of lignin
> and cellulose

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