VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 21 2009 - 16:30:30 CDT

Hi,
  Can you do the same sequence of operations, but start out by doing
these two commands first? This will help determine what's going on there:
  pwd
  glob *

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 21, 2009 at 02:26:04PM -0700, Carmen Valladares wrote:
> Hello,
> I am also stuck in the same spot in the tutorial.
> -I wrote the file in notepad
> -saved a copy as ubq.txt and copied, pasted, and renamed another as
> ubq.pgn
> so I have two files under 1-1-build
> -typed
> >Main< (VMD) 5 % source ubq.pgn
> couldn't read file "ubq.pgn": no such file or directory
> -typed each comand individually
> >Main< (VMD) 6 % package require psfgen
> 1.4.7
> >Main< (VMD) 7 % topology top_all27_prot_lipid.inp
> MOLECULE MISSING! Use resetpsf to start over.
> >Main< (VMD) 8 % resetpsf
> clearing structure, preserving topology and aliases
> -tried once more
> >Main< (VMD) 9 % source ubq.pgn
> couldn't read file "ubq.pgn": no such file or directory
> I am sure I'm in the right directory. Is there anything else I'm missing
> in order to get this to work?
> Thank you for your help
> --
> Carmen Valladares
> cjvalladares_at_ucdavis.edu
> ~~~~~~~~~~~~~~~~~~~~~~~~~~
> University of California, Davis
> College of Engineering -
> Biological Systems Engineering
>
> ---------- Forwarded message ----------
> Date: Thu, 9 Nov 2006 17:13:21 +0100
> From: Javaria Ahmed <javah_at_itn.liu.se>
> To: owner-tutorial-l_at_ks.uiuc.edu
> Subject: RE: NAMD tutorial for Windows problem reading pgn file from vmd
> tkconsole
>
> Wordpad, saved as text document , it generates the message: MOLECULE
> MISSING! Use resetpsf to start over.
>
> -----Original Message-----
> From: Javaria Ahmed
> Sent: Thu 11/9/2006 5:07 PM
> To: owner-tutorial-l_at_mailhost.ks.uiuc.edu
> Cc:
> Subject: NAMD tutorial for Windows problem reading pgn file from vmd
> tkconsole
>
> hi
>
> I am a starter.
>
> I downloaded NAMD tutorial for Windows Version October 2006.
> In section, basics of namd, for creating psf file, (point 6 pg 9), i wrote
> a text file and saved as pgn as instructed. Then I am using the command
> %source filname.pgn. But its not working. Text file with encoding ANSI,
> generates message:filename.pgn no file or directory. When i save text file
> as encoding - unicode , the message is ; invalid command name
> "ythpackage".
>
> Which formate and text editor , vmd - tkconsole supports on windows.
>
> regards,
>
> Javaria 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078