VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Mon Nov 27 2006 - 21:44:22 CST

Jan:
   here are the log files that generate the problem on paratool
related to namdserver
###################################################################
can not find channel named "0"
can not find channel named "0"
    while executing
"puts $sock "compute_coordset $dcdfile $elabel""
    (procedure "::NAMDserver::namd_compute_energies" line 5)
    invoked from within
"::NAMDserver::namd_compute_energies $namdserver $dcdfile TOTAL"
    (procedure "::Paratool::Energy::compute_derivatives" line 167)
    invoked from within
"::Paratool::Energy::compute_derivatives $intcoorlist -rebuild"
    (procedure "::Paratool::Hessian::compute_force_constants_from_inthessian"
line 204)
    invoked from within
"::Paratool::Hessian::compute_force_constants_from_inthessian"
    ("SIP" arm line 33)
    invoked from within
"switch $type {
      OPT {
         variable molidopt $newmolid
         # The join in the next line is necessary to make it work on windoze, too.
         variable molna..."
    (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)
###################################################################

Tks a lot

Daniel

On 11/20/06, Jan Saam <jan.saam_at_charite.de> wrote:
> Daniel,
>
> I think I saw this error once before with my files and I believe it had to
> something do with the input.
> Could you please send me the files you used to produce the error and tell
> me what you exactly did?
>
> Thanks,
> Jan
>
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> Germany
>
> +49 30 450-528-446
> saam_at_charite.de
>
> > 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
> >
>
>
> 

-- 
saludos desde el fin del mundo