VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 12 2012 - 15:36:25 CDT
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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)
-- 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
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