VMD-L Mailing List

From: sstappa_at_uwm.edu
Date: Thu Jul 06 2006 - 19:59:31 CDT

Hi John (and whoever else it may concern),

I was browsing back postings from the list and I too am experiencing the same
error as Ivana Adamovic, who started this thread on June 24th. My error log is
almost identical to hers with the exception of the name/location of the psf and
pdb files, and several line numbers. However as I'm running the Windows OpenGL
version of build 1.8.4 and she's using a Mac version, this probably explains
away the latter issue. The psf and pdb files I'm using are for ubiquitin, and
as you are aware can be -- and in my case, have been -- downloaded from
http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial-files/.

Additionally, I've tried solvating ubiquitin using Tcl/Tk as per the
instructions found on
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html,
and have had no luck with this method either. In this case, the program reports
that it cannot read in optional structural information from the ubiquitin pdb
file, and that 660 atoms is not the correct number of atoms that comprise the
protein, which doesn't make any sense. Unfortunately I cannot copy the complete
run/error text into an email, but will gladly provide a screen shot of this to
any interested party. Whatever assistance/advice you can provide on this matter
would be appreciated.

Thanks for your time,
-Shane