From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 23 2008 - 10:18:33 CDT

On Mon, 23 Jun 2008, Esben A. Gad wrote:

EG> Dear VMD-list

....

EG>
EG>
EG> ErrorDialog: ***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error:
EG> "(" unexpected
EG>
EG> I have tried both my CVS version of NAMD, and an earlier official release.

what kind of machine are your running on?
does any of your paths, i.e. the working directory or
the path to NAMD have any blanks or parenthesis in them?

cheers,
   axel.

EG>
EG> The details go:
EG> ---------------------------------------
EG> ***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error: "(" unexpected
EG> ***my path to namd***/Linux-amd64-g++/namd2: 1: Syntax error: "(" unexpected
EG> while executing
EG> "exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
EG> (procedure "namdrun" line 43)
EG> invoked from within
EG> "namdrun"
EG> (procedure "namdmain" line 76)
EG> invoked from within
EG> "namdmain"
EG> (in namespace inscope "::namdEnergy" script line 19)
EG> invoked from within
EG> "::namespace inscope ::namdEnergy {
EG> mol top $currentMol
EG> variable sel1
EG> variable sel2
EG> variable nsel
EG> set energy ""
EG> set..."
EG> invoked from within
EG> ".namdenergy.gobutton invoke"
EG> ("uplevel" body line 1)
EG> invoked from within
EG> "uplevel #0 [list $w invoke]"
EG> (procedure "tk::ButtonUp" line 22)
EG> invoked from within
EG> "tk::ButtonUp .namdenergy.gobutton
EG> "
EG> (command bound to event)
EG> -------------------------------------------
EG>
EG> I tried looking at the intermediate files output by NAMD-energy, but It
EG> all looks pretty standard. (I attached the namd-temp.namd input file
EG> generated. The log file was empty and the dcd and pdb generated looked
EG> fine).
EG>
EG> For me it looks like this problem is unrelated to my earlier PSF problem.
EG> However, from looking at the temporary files, I fear that if/when I get
EG> VMD to run NAMD for the interaction energy calculations, VMD will attempt
EG> to run NAMD using the version of my PSF that now only works in VMD, and
EG> not in NAMD.
EG>
EG> Thus, my question is two-fold:
EG> 1) What might be up with the "unexpected ")""-error?
EG> 2) Is it worth the effort, if the NAMD-energy plugin will feed NAMD a bad
EG> PSF anyway?
EG>
EG> It is unfortunately not easy for me to modify my conversion script to
EG> generate new PSF-files that comply more fully with the PSF EXT format, as
EG> the files from which they came are lost to me, for some of my older runs.
EG>
EG> Any and all help will be much appreciated
EG>
EG> Thanks again, - Esben
EG>
EG>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.