VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 26 2007 - 16:28:08 CDT

Jim,
  Can you verify that the segid/resid numbers you're querying
via the VMD atom selections are indeed in the PDB files that
you're feeding to psfgen? There may be some name manipulations
or mismatches going on there if you're expecting the verbatim
string in the PDB to match the atom selection strings etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 26, 2007 at 02:18:48PM -0600, Jim Pfaendtner wrote:
> Hello,
>
> I am trying to write a simple badwater script using tcl:
>
> set badwat [atomselect top "resname TIP3 and within 2.4 of (not
> resname TIP3)"]
> foreach segid [$badwat get segid] resid [$badwat get resid] {
> delatom $segid $resid }
>
> The selection part seems to be working correctly but the delatom loop
> is not, for each atom in the selection I get an error:
>
> "no segment XXXX" [XXXX is whatever I named the segment of water
> molecules when generating the psf/pdb file. Right now I took a small
> polypeptide and an empty box of water and read them in on top of each
> other just to make sure there are lots of overlaps. The water segid
> is H2O right now.]
>
> I am running this script in the TKConsole after loading the psf/pdb
> file over the peptide overlapping with the water box into VMD.
>
> I would prefer to run this from text mode when generating my psf/pdb,
> but I get errors with my atomselect command (no molID named top).
>
> Any help would be appreciated.
>
> Thanks,
> Jim 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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