VMD-L Mailing List

From: Kovács, Sándor Ádám (skovacs_at_wustl.edu)
Date: Mon Mar 15 2010 - 16:54:39 CDT

Will,

Thinking it may have been something with our use or build of g09, I ran a QM Geometry Optimization of a small test molecule (ethanol) on both g09 and g03.
After comparing the g09 output with g03 output and finding no remarkable differences, I returned to Paratool.
Paratool was able to "read-in" the output of g09 without incident, resulting in a successful paramaterization.

This topic of "(can't use non-numeric string as operand of "-")" has come up before in the mailing list as recently as December 2008, but doesn't seem to have been resolved.

I invite other thoughts and welcome suggestions.

Sándor

Ph.D. Candidate
Department of Energy, Environmental and Chemical Engineering
Washington University in St. Louis

On Sat Mar 13 2010 - 16:19:08 CST, Will Bricker wrote:
>
>Hi All,
>
>I am trying to parameterize a peridinin molecule to later run MD
>simulations. Using paratool, I created a gaussian log file of the molecule's
>optimized geometry. However, when I try to load this file into the base .pdb
>file, it sends me the following error message:
>
>can't use non-numeric string as operand of "-"
>can't use non-numeric string as operand of "-"
> while executing
>"expr {[lindex $line 0]-1}"
> (procedure "read_gaussian_mulliken" line 37)
> invoked from within
>"read_gaussian_mulliken $fid"
> (procedure "read_gaussian_cartesians" line 30)
> invoked from within
>"read_gaussian_cartesians $fid $tmppdb all"
> (procedure "read_gaussian_log" line 243)
> invoked from within
>"read_gaussian_log $file $molid"
> (procedure "load_gaussian_log" line 17)
> invoked from within
>"load_gaussian_log $file"
> (procedure "::QMtool::load_file" line 10)
> invoked from within
>"::QMtool::load_file $file [string range [file extension $file] 1 end]"
> (procedure "load_molecule" line 14)
> invoked from within
>"load_molecule OPT $file"
> (procedure "::Paratool::opendialog" line 128)
> invoked from within
>"::Paratool::opendialog loadoptgeom "[file rootname
>${::Paratool::molnamebase}]_opt""
> invoked from within
>".paratool.#paratool#menu.#paratool#menu#file invoke active"
> ("uplevel" body line 1)
> invoked from within
>"uplevel #0 [list $w invoke active]"
> (procedure "tk::MenuInvoke" line 50)
> invoked from within
>"tk::MenuInvoke .paratool.#paratool#menu.#paratool#menu#file 1"
> (command bound to event)
>
>I have tried this multiple times without any luck. Can anyone decipher this
>error message and point me in the right direction?
>
>Thanks,
>Will Bricker
>