From: Axel Kohlmeyer (
Date: Wed Sep 14 2011 - 09:37:26 CDT

On Wed, Sep 14, 2011 at 8:22 AM, Alexandre Suman de Araujo
<> wrote:
> Hi all

hi you alone. ;)

> I'm trying to model a small molecule using the CgenFF force field with
> Paratool VMD plugin. However, when I try to load top_all36_cgenff.rtf
> topology file a receive the following error message:
> list element in quotes followed by "." instead of space
> list element in quotes followed by "." instead of space
>    while executing
> "lindex $line 0"
>    (procedure "::Toporead::read_charmm_topology" line 36)
>    invoked from within
> "::Toporead::read_charmm_topology $file"
>    (procedure "::Paratool::opendialog" line 112)
>    invoked from within
> "::Paratool::opendialog topo"
>    invoked from within
> ".paratool.topo.list.buttons.add invoke"
>    ("uplevel" body line 1)
>    invoked from within
> "uplevel #0 [list $w invoke]"
>    (procedure "tk::ButtonUp" line 22)
>    invoked from within
> "tk::ButtonUp .paratool.topo.list.buttons.add"
>    (command bound to event)
> So I ask: Does Paratool support CgenFF?

obviously not. is it advertised somewhere that it should?

> If yes, does anyone could help me with this error message?

apparently, the parser for topology files cannot parse
the file that you provided. i am not an expert in this
plugin, so i cannot tell whether your file is at fault or
whether the plugin makes too many assumptions about
the file format.

> If no, someone could tell me if Paratool is still under development or
> not, since the author (Jam Saam) web page indicated in paratool page in
> VMD website ( does not
> exist anymore? There is any plan to implement CgenFF support in Paratool?

outside of the on an off bugfix to address specific technical
problems, there has been no regular development on paratool
for quite a while, since the principal author moved to a position,
where he/she doesn't have the time (and/or the need) to develop
and support the plugin. it is not the only plugin in VMD with such
a fate. you are most welcome to adopt and improve it. the
continued success of VMD depends on "people with a need"
that are willing to spend some time to get their problem solved.


> Cheers
> --
> Alexandre Suman de Araujo

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.