From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Fri Nov 30 2007 - 15:51:53 CST
I was under the impression that Paratool used Gausian to perform the
Calculations... if not, I'm a bit up the creek!
Phil
Quoting Tianjiao Wang <tjwang_at_iastate.edu>:
> Hello,
>
> 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}]
> _opt""
> (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
>
>
> Tianjiao Wang
> Rm 3288 MBB
> Iowa State Univ
> Ames, IA 50010
> e-mail: tjwang_at_iastate.edu
> tel: 515-441-6417(cell)
> 515-294-5682(O)
>
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