VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Feb 25 2011 - 07:59:56 CST

Peter and John:
Beg pardon for wasting your time. While reorganizing to follow Peter's
suggestions, I discovered (with horror) a couple or rows with two
Amber names, ASH and GLH, still in the pdb file edited for CHARMM.
Those names had created the mess.

Renaming those two residues ASP and GLU, autopsf automatically created
correctly all DISU. Then all ASPP and GLUP patches could be added
manually. The psf/pdb files, created on "Apply patches..", could be
loaded to VMD without warnings. I have not checked further so far, but
everything seems to be in order.

Debian GNU/LINUX i386 and VMD 1.9beta1 were used.

Thanks
francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Feb 25, 2011 at 6:49 AM
Subject: Re: vmd-l: autopsf-patches C++ error 'expected integer but got "" ""'
To: Peter Freddolino <petefred_at_ks.uiuc.edu>

Hi Peter:
Lately I was also thinking to the command line version because of the
repeatability, but was now waiting for what could have been a quick
repair of the gui. Now I'll follow your suggestions in steps. If still
problematic, I'll also try at 64bit. All that with the 1.9beta1
version, unless you suggest 1.8.7.

> Does it happen with one in particular?

I would say no. Although with 1.8.7 hanging occurred at 3/4 setting of
patches, with 1.9beta1 all patches could be submitted and it was the
final command that led to crash.

cheers
francesco

On Fri, Feb 25, 2011 at 4:28 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Francesco,
> For what it's worth, this is a tcl error, not c++.
>
> In any case, I haven't been able to reproduce this, so I really need a
> minimal set of steps to get it (preferrably not involving typing in 20
> patches -- incidentally, if you have a lot of patches you may wish to
> use the command line version of autopsf to make your procedure more
> repeatable and easier to edit). Can you get it with just a couple
> patches? Does it happen with one in particular? What structure are you
> working on? I've used autopsf before on structures requiring hundreds of
> ASPP/GLUP patches, but that was the command line version, so either
> there's something peculiar to your structure going on here, or there's a
> bug that only shows up in the GUI.
>
> Thanks,
> Peter
>
> On 02/23/2011 04:03 PM, 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
>>>
>