Start up vmd by double clicking its icon.
In the Tk console do a cd to the 1-1-build directory.
e.g., cd ~/Desktop/namd-tutorial-files/1-1-build/
Do steps 2-4 on pages 3-4 but do not quit VMD.
Enter
  source ubq.tcl
where you have prepared ubq.tcl as follows:

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
writepsf ubq.psf

Enter
   source wsphere.tcl
where you have commented out the exit statement.
Continue with 1.3.2 on page 11.