VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 14 2006 - 13:21:22 CDT

Hi,
  The current version of the VMD babel-based automatic translation plugin
was written for use with Babel version 1.6 (from OpenEye).
The new "OpenBabel" project uses different command line arguments (as you
see from the error below) and won't (currently) work with the babel plugin.
I've written a new branch of code into the VMD babel plugin for use with
OpenBabel, but had not made it active yet as I was waiting for some bugs
to be fixed with OpenBabel, and I haven't yet had time to re-test this
and see if it's stable enough to replace the old Babel 1.6 code yet.
You can get Babel 1.6 from OpenEye here:
  http://www.eyesopen.com/products/applications/babel.html

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 14, 2006 at 02:13:33PM -0400, dimka wrote:
> I have a similar problem with loading optimization output of Gaussian
> '98 RevA. Loading with VMD as either Gaussian92output or -94output I
> get this error:
>
> Open Babel 2.0.0 -- Mar 21 2006 -- 02:23:17
> Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
> Try -H option for more information.
> Babel molecule file translation failed!
> ERROR) Could not read file /home/dimka/opt5.log
>
> trying the same thing with qmtool, I also get an error:
>
> Error: can't use non-numeric string as operand of "*"
> can't use non-numeric string as operand of "*"
> can't use non-numeric string as operand of "*"
> while executing
> "expr {$scansteps*$scanstepsize}"
> (procedure "read_zmat_intcoor" line 33)
> invoked from within
> "read_zmat_intcoor $fid $ncoords $termstring"
> (procedure "read_zmatrix" line 137)
> invoked from within
> "read_zmatrix $fid "Recover connectivity data from disk.""
> (procedure "read_gaussian_log" line 157)
> invoked from within
> "read_gaussian_log $file $molid"
> (procedure "load_gaussian_log" line 17)
> invoked from within
> "load_gaussian_log $file"
> ("log" arm line 1)
> invoked from within
> "switch $type {
> int { read_intcoords $file; }
> zmt { set molid [read_zmtfile $file] }
> com { set molid [read_gaussian_input $file] }
> ..."
> (procedure "load_file" line 6)
> invoked from within
> "load_file $file $type "
> ("default" arm line 1)
> invoked from within
> "switch $type {
> writeint { write_intcoords $file }
> writeselint { write_intcoords $file -sel $sel }
> writecom { write_gaussian_input $file..."
> (procedure "::QMtool::opendialog" line 69)
> invoked from within
> "::QMtool::opendialog log"
> invoked from within
> ".qmtool.#qmtool#menu.#qmtool#menu#file.#qmtool#menu#file#open invoke
> active"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke active]"
> (procedure "tk::MenuInvoke" line 47)
> invoked from within
> "tk::MenuInvoke
> .qmtool.#qmtool#menu.#qmtool#menu#file.#qmtool#menu#file#open 1
> "
> (command bound to event)
>
> On 9/14/06, Francesca Mocci <francy_at_mail.dsc.unica.it> wrote:
> >
> > Hi Jan,
> >
> > thanx a lot for your prompt advice:
> >
> > - either deleting in the g03 log file the column of "Atomic Type"
> > which consist of 0s and then loading it as a gaussian94output
> > - either loading the unmodified g03 log file through the plugin QMtool
> > found in the simulation submenu of the extension menu
> > the file is loaded correctly.
> >
> > Francesca
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078