VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Sep 28 2011 - 09:39:23 CDT

Put this block before "set keyword" in readcharmmtop.tcl

      set comment [string trimleft [string range $line [expr [string first "!" $line] + 1] end]]
      if { [string first "!" $line] != -1 } {
         set line [string range $line 0 [expr [string first "!" $line] - 1]]
      }

and comment out the "set comment" line that comes up later.

On Sep 28, 2011, at 9:28 AM, Alexandre Suman de Araujo wrote:

> 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
>>