VMD-L Mailing List

From: saam (saam_at_ks.uiuc.edu)
Date: Sat May 09 2009 - 08:06:00 CDT

Sabine,

did you prepare the input for the frequency calculation manually or
was it prepared through paratool?
The Gaussian file parser has limited capabilities and maybe it
stumbled over something it didn't understand.
I can test it if you send me both Gaussian logfiles (the optimization
and the frequency calculation) and the initial structure (the file you
loaded as "Basemolecule").
If you send it to my address instead vmd-l you should not suffer from
the size limit.

Jan

On Fri, May 8, 2009 at 6:12 PM, Sabine Leroch <sabine.leroch_at_boku.ac.at> wrote:
>
>
> Dear all
>
> I am using paratool of vmd-1.8.6 togheter with Gaussian03 log files.
>
> I followed the procedure described in the paratool tutorial. When I load the
> Hessian from the single point calculation I receive the following error:
>
> domain error: argument not in valid range
>
> while executing
>
> "expr {acos($dot)}"
>
> (procedure "::QMtool::measure_dihed" line 28)
>
> invoked from within
>
> "::QMtool::measure_[lindex $zmat $j 1] $molidbase [lindex $zmat $j 2] [list
> $icenter $iupper"
>
> (procedure
> "::Paratool::Hessian::compute_force_constants_from_inthessian" line 88)
>
> invoked from within
>
> "::Paratool::Hessian::compute_force_constants_from_inthessian"
>
> ("SIP" arm line 43)
>
> invoked from within
>
> "switch $type {
>
> OPT {
>
> variable molidopt $newmolid
>
> # The join in the next line is necessary to make it work on
> windoze, too.
>
> variable molna..."
>
> (procedure "load_molecule" line 72)
>
> invoked from within
>
> "load_molecule SIP $file"
>
> (procedure "::Paratool::opendialog" line 131)
>
> invoked from within
>
> "::Paratool::opendialog loadsip "[file rootname
> ${::Paratool::molnamebase}]_sp""
>
> invoked from within
>
> ".paratool.#paratool#menu.#paratool#menu#hessian 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 .paratool.#paratool#menu.#paratool#menu#hessian 1
>
> "
>
>
>
> Unfortunately because of size problems (2MB) it was not possible to attached
> the Gaussian log file.
>
> Hope somebody can help me.
>
> Thank you
>
> Best regards
>
> Sabine
>
> *****************************************
> Dr. Sabine Leroch
> Universität für Bodenkultur
> Institut für Verfahrens- und Energietechnik
> Muthgasse 107
> A-1190 Wien
> Tel: 0043 (0)1/3709726-203
>
> ******************************************
>
>
>
>
>
>
> 

-- 
****************************************
Jan Saam
Theoretical and Computational Biophysics Group 3061 Beckman Institute
University of Illinois
405 N. Mathews Ave
Urbana, IL 61801
Phone: (217) 244-1928
Fax:   (217) 244-6078
saam_at_ks.uiuc.edu