From: Chris Harrison (charris5_at_gmail.com)
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
> 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?
-- 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 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:46 CST