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

From: Chris Harrison (
Date: Mon Mar 19 2012 - 01:40:57 CDT


What happens if you open the TkConsole, cd to the correct directory, and

mol new setup.psf
mol addfile zero.fep


On Mon, Mar 19, 2012 at 1:20 AM, Alisha "Jonesy" Jones

> Hello,
> 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?
> Regards,
> Alisha

Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078                          Fax: 217-244-6078

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