VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Mon Nov 20 2006 - 19:31:45 CST

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
>