From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 14 2007 - 20:40:06 CST

francesco,

which version of combine.tcl (there must be hundreds of scripts
under that name. i have at least five on my machine) are you
using and how, if at all, did you modify it.

by not showing the script code you were using, only those people
can help you, who know it and know which particular version you
are using. if you want to increase your chances to get help, you
have to help us by providing more information, even if they seem
redundant or obvious to you. it is very hard to give advice without
context.

regards,
   axel.

On 11/14/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> I am in a silly loop, trying to merge protein and POPC membrane and removing
> superimposition.
>
> I created a 100x100A POPC (less is not enough for my protein) and inserted and
> centered the protein.
>
> Saved protein_aligned.pdb. fed to the working directory both scripts
> combine.tcl and top_all27_prot_lipid.inp.
>
> The, at
>
> vmd -dispdev text < combine.tcl |tee combine.log

>
> the error was:
>
> There is no 'top' molecule in atom select's 'molId' (VMD 1.8.6).
>
> After resetpsf, I tried various (clearly faulty) selections with no success.
>
> Thanks for helping
> francesco pietra
>
> Incidentally, does 10x100 cause steric clashes?
>
>
> ____________________________________________________________________________________
> Never miss a thing. Make Yahoo your home page.
> http://www.yahoo.com/r/hs
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
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If you make something idiot-proof, the universe creates a better idiot.