paratool for MG

From: Tianjiao Wang (
Date: Fri Nov 30 2007 - 12:48:05 CST


  I am trying to use paratool from VMD 1.8.6 to generate topology and
parameter files for malachite green (MG) simulation in NAMD. I first loaded
MG.pdb as base molecules. Then I eidted atom properties. I loaded
top_all27_prot_na.rtf as topology file and Par_all27_prot_na.prm as parameter
files. Optimized geometry and single point calc (Hessian + charges) were done
In GAMESS. When I tried to import geometry log file from GAMESS into paratool
main, I got error message as followed:

list index out of range
list index out of range
    while executing
"lset zmat 0 4 $ndihed "
    (procedure "find_improper_dihedrals" line 22)
    invoked from within
"find_improper_dihedrals $zmat"
    (procedure "read_gaussian_log" line 191)
    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 "::QMtool::load_file" line 6)
    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}]
    (menu invoke)

Could anybody give me some advice how to solve this problem? Alternatively,
are there other ways to generate par_ and top_ file for malachite green, an
organic dye (MW:329 dalton).

Thanks a lot!


Tianjiao Wang
Rm 3288 MBB
Iowa State Univ
Ames, IA 50010
tel: 515-441-6417(cell)

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