VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 11 2011 - 09:48:57 CST

Hi Bjoern,
  Can you try using the RMSD Trajectory Tool instead of the older RMSD plugin?
The RMSDTT plugin shouldn't have this problem as far as I know.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 11, 2011 at 12:52:11PM +0100, Bjoern Olausson wrote:
> Hi,
>
> I am loading a bunch of small peptides into VMD an noticed, that the RMSD Tool
> fails when the Molecule ID is above 999.
>
> It bails out with the following message:
>
> expected integer but got "1000candidate_02624_13706.pdb"Not valid molecule id
> 1000candidate_02624_13706.pdb in atomselect's 'molId'
> expected integer but got "1000candidate_02624_13706.pdb"Not valid molecule id
> 1000candidate_02624_13706.pdb in atomselect's 'molId'
> while executing
> "atomselect $i $sel_text"
> (procedure "compute_rms" line 14)
> invoked from within
> "compute_rms $rmsd_base [concat "(" $rms_sel ") and backbone"]"
> (in namespace inscope "::RMSDTool" script line 1)
> invoked from within
> "::namespace inscope ::RMSDTool { if { $bb_only } { set tot_rms [compute_rms
> $rmsd_base [concat "(" $rms_sel ") and backbone"]] } else { set tot_rm..."
> invoked from within
> ".rmsdtool.top.right.rmsd invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .rmsdtool.top.right.rmsd"
> (command bound to event)
>
> Is there a way to reset the Molecule ID or another quick workaround?
>
> Cheers,
> Bjoern
>
>
> --
> Bjoern Olausson
> Martin-Luther-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078