VMD-L Mailing List

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Tue Dec 04 2007 - 05:18:08 CST

--- Syed Tarique Moin <tarisyed_at_yahoo.com> wrote:

> Date: Wed, 28 Nov 2007 22:01:06 -0800 (PST)
> From: Syed Tarique Moin <tarisyed_at_yahoo.com>
> Subject: Re: Paratool in VMD
> To: Jan Saam <saam_at_charite.de>
>
> Thanks its working but now i want to import this
> hessian single point log file when i try to load it
> by
> paratool it is giving the following msg.
>
> list index out of range,
>
> and the complete log is as follows:
>
> 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 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
> "
> (command bound to event)
>
>
> Regards and thanks for your fruitful cooperation for
> me
>
>
>
> Inded
> --- Jan Saam <saam_at_charite.de> wrote:
>
> > Tarique,
> >
> > this input file looks ok. Due to the
> Geom=AllCheck,
> > the complete
> > molecule specification, including coordinates, is
> > taken from the
> > checkpoint file that is specified in the line
> > starting with %chk.
> >
> > Jan
> >
> > Syed Tarique Moin wrote:
> > > Hello,
> > >
> > > Kindly you can give me some guidance that i am
> > trying
> > > to prepare input from the previously
> geometrically
> > > optimized file and want to run for the hessian
> > single
> > > point calculation but when i prepare this file
> for
> > > single point calculation that only give only
> basis
> > > sets and key words and no input coordinate for
> > next
> > > calculation.
> > >
> > > It is as follows.
> > >
> > > %chk=new_cu_sp_new.chk
> > > %nproc=1
> > > %mem=1GB
> > > # UHF/6-31G* Geom=(AllCheck,NewRedundant) Freq
> > NoSymm
> > > Pop=(ESP,NPA) IOp(6/33=2,7/33=1) SCF=Tight
> > >
> > > and no coordinate here
> > >
> > > Tarique
> > >
> > >
> >
> >
> > --
> >
> > ****************************************
> > 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
> >
> >
> >
>
>
>
>
>
____________________________________________________________________________________
> Never miss a thing. Make Yahoo your home page.
> http://www.yahoo.com/r/hs
>

      ____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs