VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Sat Mar 10 2012 - 15:14:20 CST

I found where the problem is:

in "/Applications/VMD 1.9.1.app/Contents/vmd/plugins/noarch/tcl/qmtool1.3"

qmtool_readwrite.tcl

proc ::QMtool::read_gaussian_mulliken { fid }

There are several "bugs" probably for Gaussian 09 outputs:

1. "Sum of Mulliken charges=*" should be "Sum of Mulliken atomic charges =*"
2. The error message I got initially was from this line: set index [expr {[lindex $line 0]-1}]
    Somehow the error went away if I "set numList [lindex $line 0]" and then "set index [expr {$numList-1}]"
3. The second "Sum of Mulliken charges=*" should be "Sum of Mulliken charges with hydrogens summed into heavy atoms =*"

After correcting these three places, Gaussian 09 log files were loaded without errors.

___________________________

Yi (Yves) Wang
Duke University

On 2012-3-10, at 下午2:58, Wang Yi wrote:

> Dear VMD users/experts,
>
> I have been trying to use the Force field toolkit in VMD 1.9.1 (Mac) to parameterize a new molecule. In the "Water Int." tab, I created several Gaussian input files and finished running them with Gaussian 09. Then when I tried to load the log files, I got 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 "::QMtool::read_gaussian_log" line 243)
> invoked from within
> "::QMtool::read_gaussian_log $logfile $molId"
> ("foreach" body line 5)
> invoked from within
> "foreach logfile $::ForceFieldToolKit::gui::gzmLOGfiles {
> set molId [mol new]
> ::QMtool::use_vmd_molecule $molId..."
> invoked from within
> ".fftk_gui.hlf.nb.genzmat.run.loadLOG invoke "
> invoked from within
> ".fftk_gui.hlf.nb.genzmat.run.loadLOG instate {pressed !disabled} { .fftk_gui.hlf.nb.genzmat.run.loadLOG state !pressed; .fftk_gui.hlf.nb.genzmat.run.l..."
> (command bound to event)
>
>
> Looks like there are issues associated with reading the Mulliken Charges. In the previous tab of "Geometry optimization", ffTK has no problem of extracting the optimized geometry from the Gaussian 09 log file. So I guess the problem is about Mulliken charge. Here's the input headers of the Gaussian files:
>
> %chk=T6AM-DON-HO2.chk
> %nproc=8
> %mem=3GB
> # RHF/6-31G* Opt=(Z-matrix,MaxCycles=100)
>
> <qmtool> simtype="Geometry optimization" </qmtool>
> T6AM-DON-HO2
>
> 2 1
>
> (2 positive charges).
>
> I don't have access to Gaussian 03 any more, to test whether the issue is about version incompatibility. How should I modify the output format for ffTK to correctly parse the file? Thanks a lot~
>
> Best,
>
>
> ___________________________
>
> Yves Wang
> Duke University
>
>
>
>
>