VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 14 2011 - 10:10:31 CDT

Hi,
  Paratool was not designed to handle CgenFF, and at present there are
no immediate plans to update the code for it. If this is merely an
issue with parsing the topology file, it is conceivable it may be
addressed at a later time during other updates, but I can't promise
anything currently.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 14, 2011 at 09:22:33AM -0300, Alexandre Suman de Araujo wrote:
> Hi all
>
> 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?
>
> If yes, does anyone could help me with this error message?
>
> 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 (http://bioinf.charite.de/biophys/people/saam) does not
> exist anymore? There is any plan to implement CgenFF support in Paratool?
>
> Cheers
>
> --
> Alexandre Suman de Araujo
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078