VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Dec 02 2011 - 11:37:38 CST

Debug it by putting print statements throughout the script that output
something like "check1", "check2", etc. Wherever the print statements
begin to fail to output during a run will indicate where in the script
the problem is located.

Best,
Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Molybdos Kirkimpolakis <supercomputer.simulation_at_gmail.com> writes:
> Date: Fri, 2 Dec 2011 11:34:27 -0500
> From: Molybdos Kirkimpolakis <supercomputer.simulation_at_gmail.com>
> To: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Reading the SMD information form the log file
> 
> Dear VMD Master,
> 
> I was wondering if my last post should be posted in namd list? I am still
> strugguling with this tcl script that is not working. Can anyone please
> point why I am getting the error of "unmatched open brace in list". I
> checked and it seems that there is no missing brace.
> 
> Thanks so much.
> 
> Here is the script.
> 
> #####################################
> > ### Open the log file for reading and the output .dat file for writing
> > set file [open SMD.log r]
> > set output [open analysis/force.dat w]
> >
> > ### Loop over all lines of the log file
> > set file [open SMD.log r]
> > while { [gets $file line] != -1 } {
> > ### Determine if a line contains SMD output. If so, write the
> > ### timestep followed by f(dot)n to the output file
> >     if {[lindex $line 0] == "SMD"} {
> >        puts $output "[lindex $line 1] [lindex $line 5] [lindex $line 6]
> > [lindex $line 7]"
> >        }
> >  }
> >
> > ### Close the log file and the output .dat file
> > close $file
> > close $output
> > #######################################################################
> 
> 
> 
> 2011/11/30 Molybdos Kirkimpolakis <supercomputer.simulation_at_gmail.com>
> 
> > Dear VMD Masters,
> > I'm trying to read the SMD information from the log file; using the tcl
> > script provided by namd tutorial; however I am geting the follwing error
> >
> > unmatched open brace in list
> >
> > Can someone tell me what is wrong?
> >
> > Thanks so much for your help.
> >
> > Here is the script.
> >
> > ###################################################################
> > ### Open the log file for reading and the output .dat file for writing
> > set file [open SMD.log r]
> > set output [open analysis/force.dat w]
> >
> > ### Gather input from user.
> >
> >
> > ### Loop over all lines of the log file
> > set file [open SMD.log r]
> > while { [gets $file line] != -1 } {
> > ### Determine if a line contains SMD output. If so, write the
> > ### timestep followed by f(dot)n to the output file
> >     if {[lindex $line 0] == "SMD"} {
> >        puts $output "[lindex $line 1] [lindex $line 5] [lindex $line 6]
> > [lindex $line 7]"
> >        }
> >  }
> >
> > ### Close the log file and the output .dat file
> > close $file
> > close $output
> > #######################################################################
> >
> >
> > --
> > cheers
> >
> > Molybdos Kirkimpolakis
> >
> > Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr>
> >
> > ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ
> >
> >
> >
> 
> 
> -- 
> cheers
> 
> Molybdos Kirkimpolakis
> 
> Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr>
> 
> ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ