From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Sep 15 2009 - 11:32:35 CDT

Based on the error message that you have provided, it looks like the segment ID
is not getting set for the molecule you are working with. That information is
provided by the PSF file, so it definitely appears that the lack of a PSF file
is your problem. You can the AutoPSF tool from Extensions | Modeling to create
a PSF file if needed.

Kirby

wuxiao wrote:
> Hello,
> Thanks a lot for your attention!
>
> > Date: Mon, 14 Sep 2009 14:16:24 -0500
> > From: kvandivo_at_ks.uiuc.edu
> > To: xiaowu759_at_hotmail.com
> > CC: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: CGTools error: atom select: cannot parse
> selection text...
> >
> > wuxiao wrote:
> > > Dear VMDers,
> > > I try to use the CGTools to convert the all-atom model to the
> > > corresponding CG model. Only to find some errors are given: atom
> select:
> > > cannot parse selection text....
> > > Can this be due to the format of cgc file? Or is the psf file needed
> > > for running the CGTools?
> > > Thank you for any reply to this post.
> >
> > Hello,
> >
> > If you could provide more information, that would be very helpful in
> diagnosing
> > the problem you are seeing.
> >
> > Are you trying to do shape based, or residue based?
> residue based RBCG
> > What molecule are you working with?
> A arbitrary molecule, tetramer of vinyl alcohol with three types of
> residues named AAA, BBB, CCC
> > Any other relevant info you can provide?
> All error messeage are as follows
> atomselect: cannot parse selection text: occupancy >= 0 and segid and
> ( index 7 or { name H11 and resid 2 and resname BBB } or { name H12 and
> resid 2 and resname BBB } or { name C2 and resid 2 and resname BBB }
> or { name H21 and resid 2 and resname BBB } or { name O3 and resid 2
> and resname BBB } or { name H31 and resid 2 and resname BBB } )
> atomselect: cannot parse selection text: occupancy >= 0 and segid and
> ( index 7 or { name H11 and resid 2 and resname BBB } or { name H12 and
> resid 2 and resname BBB } or { name C2 and resid 2 and resname BBB }
> or { name H21 and resid 2 and resname BBB } or { name O3 and resid 2
> and resname BBB } or { name H31 and resid 2 and resname BBB } )
> while executing
> "atomselect $molid "$fullbeadsel""
> (procedure "apply_bead" line 66)
> invoked from within
> "apply_bead $cgbead $molid $rcgout"
> (procedure "::cgtools::apply_database" line 26)
> invoked from within
> "::cgtools::apply_database $::cggui::currentToCGMol
> $::cggui::toCGoutpdbfile $::cggui::revcgfile"
> (procedure "::cggui::buildResidueCGExecute" line 43)
> invoked from within
> "::cggui::buildResidueCGExecute"
> invoked from within
> ".cggui.toCGResidueFrame.applyDB invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .cggui.toCGResidueFrame.applyDB"
> (command bound to event)
> >
> > Thanks,
> >
> > --
> >
> > Kirby Vandivort Theoretical and
> > Senior Research Programmer Computational Biophysics
> > Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
> > http://www.ks.uiuc.edu/~kvandivo/ Unive rsity of Illinois
> > Phone: (217) 244-1928 405 N. Mathews Ave
> > Fax : (217) 244-6078 Urbana, IL 61801, USA
>
>
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-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA