From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 09 2015 - 13:25:36 CST

On Mon, Feb 9, 2015 at 2:07 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Feb 9, 2015 at 1:43 PM, Ben Hanson <ben19q_at_hotmail.com> wrote:
>> The vmd version is 1.9.2 and I am unsure how to check the topotools version.
>
> package require topotools
>
> it will return the version number of the topotools plugin. however, if
> you have VMD 1.9.2, you also have the latest plugin.
>
>> I have attached the simple data file.
>
> thanks. there has to be something about it that is different from
> others and thus makes it trigger the bug you are reporting.
>
> hopefully i can get back to you soon with a bugfix.

ok. here we are. you have to edit the file topoatoms.tcl in
/usr/local/lib/vmd/plugins/noarch/tcl/topotools1.5/ (or in the
corresponding directory, if you didn't install VMD into the default
location).

in line 43, you have to replace the [ptefrommass $idx] call with
[ptefrommass $a] so that it reads:

                $s set element [lindex $elements [ptefrommass $a]]

that should take care of this bug. as far as i can tell, this was
changed only recently during some cleaning up of the code. i will also
upload a corrected version to the topotools section of my homepage.

axel.

>
> more later,
> axel.
>
>>
>> Thanks
>> Ben
>>
>>
>>> Date: Mon, 9 Feb 2015 13:37:07 -0500
>>> Subject: Re: vmd-l: topo guessatom
>>> From: akohlmey_at_gmail.com
>>> To: ben19q_at_hotmail.com
>>> CC: vmd-l_at_ks.uiuc.edu
>>
>>>
>>> On Mon, Feb 9, 2015 at 1:03 PM, Ben Hanson <ben19q_at_hotmail.com> wrote:
>>> > I have imported a lammps data file using topotools, but when I attempt
>>> > to
>>> > change types to elements using the command
>>> >
>>> > topo guessatom lammps data
>>> >
>>> > I get the error "can't read "idx": no such variable", with previous
>>> > versions
>>> > I have not had this issue. Any help would be greatly appreciated
>>>
>>> which version of topotools? which version of VMD? are both the latest?
>>>
>>> if both are the latest, can you provide a (simple) test file to
>>> reproduce the issue?
>>>
>>> axel.
>>>
>>> >
>>> > Ben Hanson
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.