VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 23 2011 - 15:03:16 CST

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
>