From: Axel Kohlmeyer (
Date: Tue Apr 29 2008 - 06:49:20 CDT

On Tue, 29 Apr 2008, wrote:

RP> Dear Axel,
RP> In your mail from 17 Apr 2008 ("Re: measure hbonds between protein and water
RP> - problem with periodic boundary conditions"
RP> <>) you
RP> advised to use
RP> pbc wrap -center "<selection text for molecule>" -all
RP> I have tried to use it from VMD Tk console and it perfectly worked but when
RP> I use it in tcl script I'm getting "invalid command name "pbs" ". Do you (or
RP> anybody else) have any idea why it can happen.

dear regina,

you have a typo. the command is "pbc" not "pbs".

in case you run in text mode, and the typos is in
your e-mail, you have to first "require" the pbctools
package. see your favorite TCL tutorial/book/manual for
details on what this does and how to use it.


RP> Thanks
RP> Regina

Axel Kohlmeyer
   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
If you make something idiot-proof, the universe creates a better idiot.