VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 18 2010 - 13:07:13 CDT

Hi,
  The error you're getting there is coming from the Tcl interpreter
when it runs the script that implements the membrane plugin. I can't
guess where it's coming from. In order to nail it down we'd have to
walk through the script while it runs on your specific dataset
and figure out where that error is originating from. You could do this
yourself by adding some "puts" calls in the membrane.tcl script.
Rather than spending time on this with the old version of the code however,
I would suggest that you should begin by getting the latest test version of
VMD and try the newer version of the membrane plugin and see if you still
have the same problem or not:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 18, 2010 at 11:21:07AM -0400, Lepore, Bryan wrote:
> [ vmd 1.8.7 ]
> [ ubuntu 10.4 ]
>
> vmd reports "integer value too large to represent"
>
> i do not know where to go from there.
>
> details :
>
> made a lipid-only pdb/psf box using autopsf and other things from Jeff Klauda's resources (thanks!).
> didn't find any coordinate "0.000 0.000 0.000" atoms
> looked at the pdb in VMD - atoms/bonds appear sensibly connected.
> put them into lib/vmd/plugins/noarch/tcl/membrane1.0/
> package require membrane
> membrane -l dmpc_lipid_only_psfgen_output -x 90 -y 90
> [ vmd appears to read files ok, reports sensible stats, then..]
> integer value too large to represent
> the graphics look ok, i didn't find the message in membrane.tcl, and popc works ok.
> stumped - where/what is this integer value?
>
> -bryan
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078