VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Apr 02 2013 - 16:36:47 CDT

This specific error is occurring because the segid has not been set for the PDB
file that has been loaded into VMD.

You can solve this by:

using a PDB where the segid has been set for the atoms. You can manually edit
the PDB file to include the segids, or you could use something like 'Extensions
| Automatic PSF Builder' to create compliant PDBs.

or, you can edit within VMD's memory. Something like:

set tmp [atomselect 0 all]
$tmp set segid P1

(where 'P1' is a segid name that you choose)

If you do either of these, and don't have an actual PSF file loaded, you will
(with the currently released version of CG tools) still get the warning message
about not having a PSF file loaded when you subsequently attempt to residue-base
coarse grain, but CG Tools should go ahead and create a CG representation of
your PDB file. It is up to you to determine if the results are scientifically
valid wrt the segid that you have specified in your PDB file. 'Automatic PSF
Builder', as an example, sets the segid to P1 in both the PDB and the PSF file,
so I assume it isn't too much of a problem to do this. (others can chime in if
I'm off base here)

Kirby

On 04/01/2013 11:59 PM, WuChaofu wrote:
> Dear Dong and VMDers,
> Thank you very much! I had thought so, but an error arises as presented below. Thus, this might be due to that psf file is not provided. How to deal with this problem?
> Chaofu Wu
>
> No PSF file loaded. I'll go ahead and do the coarse graining, but it might not work properly. You might want to run again after loading a PSF file.
> Apply bead with bead 228
> ERROR>syntax error
> more detail is as follows:
> atomselect: cannot parse selection text: occupancy>= 0 and segid and ( index 1 or { name H11 and resid 1 and resname tMA } or { name H12 and resid 1 and resname tMA } or { name C2 and resid 1 and resname tMA } or { name C6 and resid 1 and resname tMA } or { name H61 and resid 1 and resname tMA } or { name H62 and resid 1 and resname tMA } or { name H63 and resid 1 and resname tMA } or { name C3 and resid 1 and resname tMA } or { name O31 and resid 1 and resname tMA } or { name O4 and resid 1 and resname tMA } or { name C5 and resid 1 and resname tMA } or { name H51 and resid 1 and resname tMA } or { name H52 and resid 1 and resname tMA } or { name H53 and resid 1 and resname tMA } )
> atomselect: cannot parse selection text: occupancy>= 0 and segid and ( index 1 or { name H11 and resid 1 and resname tMA } or { name H12 and resid 1 and resname tMA } or { name C2 and resid 1 and resname tMA } or { name C6 and resid 1 and resname tMA } or { name H61 and resid 1 and resname tMA } or { name H62 and resid 1 and resname tMA } or { name H63 and resid 1 and resname tMA } or { name C3 and resid 1 and resname tMA } or { name O31 and resid 1 and resname tMA } or { name O4 and resid 1 and resname tMA } or { name C5 and resid 1 and resname tMA } or { name H51 and resid 1 and resname tMA } or { name H52 and resid 1 and resname tMA } or { name H53 and resid 1 and resname tMA } )
> 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 24)
> invoked from within
> "tk::ButtonUp .cggui.toCGResidueFrame.applyDB"
> (command bound to event)
> ________________________________
>> Date: Mon, 1 Apr 2013 08:39:56 -0700
>> From: us917_at_yahoo.com
>> Subject: Re: vmd-l: CGTools with pdb and top files
>> To: xiaowu759_at_hotmail.com
>> CC: vmd-l_at_ks.uiuc.edu
>>
>> By information on http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/,
>> I don't see why psf file is required for the AA (all-atoms) model. Only
>> pdb file is used for the conversion. No Charmm or OPLS force field
>> parameter files are needed. But you do need a psf file to run
>> simulations for newly coverted CG molecule. Just follow instructions in
>> the link.
>>
>> Dong
>>
>> ________________________________
>> From: WuChaofu<xiaowu759_at_hotmail.com>
>> To: "vmd-l_at_ks.uiuc.edu"<vmd-l_at_ks.uiuc.edu>
>> Sent: Monday, April 1, 2013 3:55 AM
>> Subject: vmd-l: CGTools with pdb and top files
>>
>> Dear VMDers,
>> I try to use the CGTools plugin to perform the conversion from AA to
>> CG. As confirmed that, both pdb and psf files are required for the AA
>> model. However, I have only a top file in the format of GROMACS instead
>> of a psf file. In the top file, all parameters are described by the
>> OPLSAA force field. How should I perform the conversion with only pdb
>> and top file in hand? Or How should I modify the tool to achieve this?
>> Please give me some hints. Thank you very much!
>> Chaofu Wu
>>
>> 

-- 
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) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA