VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 23 2011 - 16:54:55 CST

Francesco,
  We are looking into this and will get back to you if we have questions,
but this is hopefully a simple problem to fix.

Cheers,
  John

On Wed, Feb 23, 2011 at 10:03:16PM +0100, Francesco Pietra wrote:
> John:
> I tried with 1.9beta1 on my old desktop Pentium with Debian GNU/Linux
> i386. All patches could now be submitted and I am pretty sure that
> there was no error in the couples within DISU patches. However, "Apply
> patches and finish PSF/PDB" led to
>
> can't read "logfileout": no such variable
> can't read "logfileout": no such variable
> while executing
> "puts $logfileout "Applying patch: [lindex $patch 0] [lindex $patch
> 1]:[lindex $patch 2] [lindex $patch 3]:[lindex $patch 4]""
> (procedure "::autopsf::makepatches_gui" line 13)
> invoked from within
> "::autopsf::makepatches_gui"
> invoked from within
> ".autopsf.patches.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.patches.finish"
> (command bound to event)
>
> Is that lack of something from my side?
>
> Incidentally, should (in autopsf) the reorganization of dihedrals etch
> follwing the application of patches occur automatically? I remember
> vaguely that time ago there was a button (may be regen?) to do that.
>
> francesco
>
>
>
> On Wed, Feb 23, 2011 at 5:47 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Francesco,
> >  I understand.  If you can test the new code by this weekend that is
> > soon enough that if there is still a bug we might be able to address it
> > before VMD 1.9 is released.
> >
> > Cheers,
> >  John
> >
> > On Wed, Feb 23, 2011 at 05:42:55PM +0100, Francesco Pietra wrote:
> >> John:
> >> I forgot to mention that I was using 1.8.7 on Debian GNU/Linux. It
> >> will take some time to report on your suggestion because it deals of
> >> some forty patches
> >> francesco
> >>
> >> On Wed, Feb 23, 2011 at 5:34 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> > Francesco,
> >> >  Can you try using the new VMD 1.9beta1 version and see if you still
> >> > encounter this problem?  A few changes were made to autopsf that might
> >> > relate to your problem.
> >> >
> >> > Cheers,
> >> >  John
> >> >
> >> > On Wed, Feb 23, 2011 at 05:21:11PM +0100, Francesco Pietra wrote:
> >> >> Hello:
> >> >> While applying very many ASPP, GLUP, and DISU patches, at 3/4 way the
> >> >> "Autopsf - Add Patch" refuses to add further patches, reporting a
> >> >> C-typical (though for me obscure) error. Below the log:
> >> >>
> >> >> expected integer but got ""
> >> >> expected integer but got ""
> >> >>     while executing
> >> >> "format $patchformat5 [lindex $patch 0] [lindex $patch 1] [lindex
> >> >> $patch 2] [lindex $patch 3] [lindex $patch 4]"
> >> >>     (procedure "update_patchtexts" line 13)
> >> >>     invoked from within
> >> >> "update_patchtexts"
> >> >>     (procedure "::autopsf::addpatch" line 17)
> >> >>     invoked from within
> >> >> "::autopsf::addpatch"
> >> >>     invoked from within
> >> >> ".patchadder.buttons.addpatch invoke"
> >> >>     ("uplevel" body line 1)
> >> >>     invoked from within
> >> >> "uplevel #0 [list $w invoke]"
> >> >>     (procedure "tk::ButtonUp" line 22)
> >> >>     invoked from within
> >> >> "tk::ButtonUp .patchadder.buttons.addpatch"
> >> >>     (command bound to event)
> >> >>
> >> >> Unable to find a specific precedent on the web; grateful for help.
> >> >>
> >> >> thanks
> >> >> francesco pietra
> >> >
> >> > --
> >> > 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
> >> >
> >
> > --
> > 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
> > 

-- 
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