FEP tutorial-my molecule doesn't show up in VMD

From: Alisha \ (jonesan_at_muohio.edu)
Date: Mon Mar 19 2012 - 01:20:44 CDT


I am working through the FEP tutorial. I am on section 1.1 System Setup.
I am sorry for such an "basic problem" but any help would be appreciated.

When I try to run the [vmd setup.psf -pdb zero.fep] command (step 6) in my
terminal, vmd opens, but my newly created molecule does not appear. I have
checked and rechecked all of my files with the example-output folder and
everything is correct. I tried this same command in the VMD TkConsole, but
I still don't get my new hybrid.

I have the latest version of VMD and NAMD.. I don't think I need the
alchemify command (I tried it anyway; it made no difference) Does anyone
know what I could quite possibly be doing wrong?


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