VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Mon Mar 12 2012 - 15:40:12 CDT

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)