VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Mon Nov 20 2006 - 19:03:17 CST

Hi John:
   I updated the files, but now i found some problems with namdserver 1.1 "
cannot find channel 0" it said. I also probe the test procedure and didnt
works.

Thanks a lot for your help!

On 11/20/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi Daniel,
> I just did a recursive 'diff' of the version you're using and the
> latest versions Jan has checked into CVS and there are some substantial
> changes, so I'd suggest trying out the newer versions which are included
> in the plugin update I posted last week and letting us know if you still
> have this particular problem or not, unless you've already heard back
> separately from Jan on this already.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Nov 15, 2006 at 07:43:17PM -0800, daniel aguayo wrote:
> > Hi John
> > I'm using an updated version that Jan sent to me. But this bug ( and
> the
> > file mentioned) happens in all version i probe ( from vrs Paratool 1.2,
> 1.3
> > ). I'm attaching the that files.
> > Tks a lot.
> >
> > Daniel Aguayo
> >
> > On 11/15/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > >Hi Daniel,
> > > Which version of the paratool plugin are you running?
> > >Jan has been busily addressing bugs and limitations that
> > >occured in the version included with VMD 1.8.5, so if you
> > >were using the VMD 1.8.5, version, you'll want to get an
> > >updated copy. I plan to post an updated set of VMD plugins
> > >for all platforms shortly, and this will include the new
> > >version of paratool as well.
> > >
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >On Wed, Nov 15, 2006 at 11:29:58AM -0800, daniel aguayo wrote:
> > >> Dear Jan and VMD users:
> > >> I found a new bug on paratool,
> > >>
> > >> ###################################### ERROR
> > >> ###############################################
> > >> can't read "base(-1)": no such element in array
> > >> can't read "base(-1)": no such element in array
> > >> while executing
> > >> "puts "base(-1)=$base(-1); atom(-1)=$atom(-1)""
> > >> (procedure "::Paratool::Energy::make_distortion" line 41)
> > >> invoked from within
> > >> "::Paratool::Energy::make_distortion $molidbase $type [array get
> pos]
> > >> [array get atom] -dx $dx"
> > >> (procedure
> > >> "::Paratool::Hessian::compute_force_constants_from_inthessian" line
> 67)
> > >> invoked from within
> > >> "::Paratool::Hessian::compute_force_constants_from_inthessian"
> > >> ("SIP" arm line 32)
> > >> invoked from within
> > >> "switch $type {
> > >> OPT {
> > >> variable molidopt $newmolid
> > >> variable molnameopt [molinfo $newmolid get name]
> > >>
> > >> if {[llength [::QMtool::get_scfenerg..."
> > >> (procedure "load_molecule" line 72)
> > >> invoked from within
> > >> "load_molecule SIP $file"
> > >> (procedure "::Paratool::opendialog" line 131)
> > >> invoked from within
> > >> "::Paratool::opendialog loadsip "[file rootname
> > >> ${::Paratool::molnamebase}]_sp""
> > >> (menu invoke)
> > >>
> > >>
> >
> >######################################################################################################
> > >
> > >>
> >
> >######################################################################################################
> > >>
> > >>
> > >> I can trace it to the line 93 of the file paratool_energies.tcl
> > >> The problem happens when the variable base(-1) is called because its
> not
> > >
> > >> always define
> > >> as you can see here
> > >>
> > >> ########################## proc ::Paratool::Energy::make_distortion
> file
> > >> paratool_energies.tcl lines 58 - 99 ###########
> > >> # Construct selections left and right of the conformation
> > >> if {[string match "*bond" $type]} {
> > >> set inring [::Paratool::bond_in_ring $base(0) $base(1)]
> > >> if {[llength $inring]} {
> > >> puts "BOND $base(0)--$base(1) IN RING"
> > >> variable ::Paratool::ringlist
> > >> set vis {}; # will contain the two ring neighbors of atom(0)
> > >> set sel [atomselect $molidbase "index $base(0)"]
> > >> foreach nb [join [$sel getbonds]] {
> > >> if {[lsearch [lindex $ringlist $inring] $nb]>=0} {
> > >> # This neighbor of atom(0) is part of the ring
> > >> lappend vis $atomtrans($nb)
> > >> if {$nb!=$base(1)} { set base(-1) $nb }
> > >> }
> > >> }
> > >> $sel delete
> > >> set atom(-1) [::Paratool::ldiff $vis $atom(1)]
> > >> puts "base(-1)=$base(-1); atom(-1)=$atom(-1)"
> > >> set base(-2) [lindex [::Paratool::ring_order [lindex $ringlist
> > >$inring]
> > >> $base(0) $base(-1)] 2]
> > >>
> > >>
> > >>
> >
> >#############################################################################
> > >>
> > >> I'm trying yo solve it, but if you can help me i'll be very thakful
> > >>
> > >> Daniel Aguayo V.
> > >> Biochemistry Student
> > >> Andres Bello University
> > >> Santiago, Chile.
> > >> --
> > >> saludos desde el fin del mundo
> > >
> > >--
> > >NIH Resource for Macromolecular Modeling and Bioinformatics
> > >Beckman Institute for Advanced Science and Technology
> > >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/
> >
> > > Fax:
> > >217-244-6078
> > >
> >
> >
> >
> > --
> > saludos desde el fin del mundo
>
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
saludos desde el fin del mundo