From: Esben A. Gad (
Date: Mon Jun 23 2008 - 07:20:08 CDT

Dear VMD-list

Thanks for the help, Peter and Axel.

It turns out that while my particular blend of a PSF file is readable for
NAMD if-and-only-if I *include* the PSF EXT tag at the top, it is readable
for VMD if-and-only-if I *remove* the PSF EXT tag. So now I one version
that works in each program...

I realize this is getting slightly cumbersome but my troubles are not over.

I now load my PSF (no tag) into VMD and try to run the NAMD-energy
plug-in. I get:

ErrorDialog: ***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error:
"(" unexpected

I have tried both my CVS version of NAMD, and an earlier official release.

The details go:
***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error: "(" unexpected
***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error: "(" unexpected
    while executing
"exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
    (procedure "namdrun" line 43)
    invoked from within
    (procedure "namdmain" line 76)
    invoked from within
    (in namespace inscope "::namdEnergy" script line 19)
    invoked from within
"::namespace inscope ::namdEnergy {
      mol top $currentMol
      variable sel1
      variable sel2
      variable nsel
      set energy ""
    invoked from within
".namdenergy.gobutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .namdenergy.gobutton
    (command bound to event)

I tried looking at the intermediate files output by NAMD-energy, but It
all looks pretty standard. (I attached the namd-temp.namd input file
generated. The log file was empty and the dcd and pdb generated looked

For me it looks like this problem is unrelated to my earlier PSF problem.
However, from looking at the temporary files, I fear that if/when I get
VMD to run NAMD for the interaction energy calculations, VMD will attempt
to run NAMD using the version of my PSF that now only works in VMD, and
not in NAMD.

Thus, my question is two-fold:
1) What might be up with the "unexpected ")""-error?
2) Is it worth the effort, if the NAMD-energy plugin will feed NAMD a bad
PSF anyway?

It is unfortunately not easy for me to modify my conversion script to
generate new PSF-files that comply more fully with the PSF EXT format, as
the files from which they came are lost to me, for some of my older runs.

Any and all help will be much appreciated

Thanks again, - Esben

Esben A. Gad
Kristianiagade 10
DK-2100 Cph E