VMD-L Mailing List

From: Alexandre Suman de Araujo (asaraujo_at_ibilce.unesp.br)
Date: Wed Sep 28 2011 - 09:28:14 CDT

Hi.

Please, could you tell me how did you fixed the plugin? I've tried to do
this looking inside readcharmmtop.tcl file but my TCL was not enough to
perform this task.

Cheers 

-- 
Alexandre
Em 15-09-2011 03:31, JC Gumbart escreveu:
> I noticed this myself recently.  It's an issue with readcharmmtop in Topotools, not with CGenFF specifically (in this case - CGenFF still causes other issues in VMD at the moment).  If a comment has a ". in it, it causes an error.  I fixed the plugin to not get caught on this, but in the short term one can just remove the offending ". from the topology file.
>
> Although Paratool is not under active development (and was almost too ambitious to begin with, honestly), "something" to help with parametrization is coming eventually...
>
> On Sep 14, 2011, at 10:10 AM, John Stone wrote:
>
>> 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
>