VMD-L Mailing List

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Fri Aug 21 2009 - 16:40:52 CDT

I am pretty sure you are not in the correct subdirectory. Type "pwd"
to see what directory you are in, and check to make sure all the
required files are there.

Former UCD alumni here, so go Ags! =)

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

On Aug 21, 2009, at 4:26 PM, 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
> "˙ūpackage".
> Which formate and text editor , vmd - tkconsole supports on windows.
> regards,
> Javaria
>