VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Thu Sep 14 2006 - 13:13:33 CDT

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
>
>