VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 26 2008 - 16:38:07 CDT

On Wed, 26 Mar 2008, Matt Watkins wrote:

MW> Hi all,
MW>
MW> I've been struggling to use the pbc tools plugin on a system I'm trying to
MW> analyse. I want to center the view on "index 1471", but the command
MW>
MW> pbc wrap -center "index 1471"
MW>
MW> is either producing strange results or naught. This occurs for vmd.1.8.6 or
MW> the latest alpha(as of today).

matt,

that is probably because of the default of pbctools to wrap by
residue. i guess you want a wrap by atom, right? try:

pbc wrap -nocompound -center "index 1471"

...and then you probably need to recompute the bonds with:

mol bondsrecalc 0

hope this helps,
    axel.
 
MW> The file is problem.xyz.bz2 uploaded to biocore. It contains the cell
MW> parameters in the second line, which I was setting with
MW>
MW> pbc set { 26.92 31.08 59.30 }
MW>
MW> originally the file was a dlpoly_history2 file that after experiencing
MW> similar problems, I converted to xyz...if that can make any odds.
MW> ,
MW> cheers,
MW>
MW> Matt
MW> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.