VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 12 2012 - 15:44:58 CDT

Albert,
  Can you zip or tar up all of the files needed to reproduce the problem
and send a copy to Michal (the propka GUI author) and myself? I'm CCing
Michal on this email so he is aware of the discussion before you send
us the files.

Michal, let us know if you need additional information.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 12, 2012 at 09:40:12PM +0100, Albert wrote:
> Hi John:
>
> thank you very much for kind reply.
> I've just try to import the .pka file into PROPKA GUI from
> file-->load propka result file... then I get the error log....
>
> I don't use the selection box. However, I also try it but still doesn't
> work.
> best
> Albert
>
> On 03/12/2012 09:36 PM, John Stone wrote:
> >Hi,
> > I'm afraid we'll need much more information than what you have provided
> >so far in order to help. I need to be able to forward the complete
> >steps you performed to the authors of the PropKa plugin so they can check
> >it.
> >What atom selection did you use in the "show selection" box? What options
> >did you check in the PropKa GUI?
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Mon, Mar 12, 2012 at 09:24:37PM +0100, Albert wrote:
> >> Dear:
> >> I've performed propka3.1 by command in terminal and it was finished
> >> normally. I am trying to import the results into VMD 1.91 but it said
> >> the
> >> following:
> >>
> >> atomselect: cannot parse selection text: resname<1> and name O32
> >> atomselect: cannot parse selection text: resname<1> and name O32
> >> while executing
> >> "atomselect $mol "resname $tmpname and name $tmpid$tmpchain_seltext""
> >> (procedure "::PropKa::propka_getLigandID" line 24)
> >> invoked from within
> >> "::PropKa::propka_getLigandID $resid [lrange $line 10 13]"
> >> (procedure "::PropKa::propka3_read" line 312)
> >> invoked from within
> >> "::PropKa::propka3_read"
> >> (procedure "::PropKa::propka_results" line 55)
> >> invoked from within
> >> "::PropKa::propka_results"
> >> ("foreach" body line 6)
> >> invoked from within
> >> "foreach tmpfile $filetest {
> >> set ::PropKa::pkafile $tmpfile
> >> set ::PropKa::jobdir [file dirname $::PropKa::pkafile]
> >> ..."
> >> invoked from within
> >> ".propka.menubar.file.menu invoke active"
> >> ("uplevel" body line 1)
> >> invoked from within
> >> "uplevel #0 [list $w invoke active]"
> >> (procedure "tk::MenuInvoke" line 50)
> >> invoked from within
> >> "tk::MenuInvoke .propka.menubar.file.menu 1"
> >> (command bound to event) 

-- 
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