VMD-L Mailing List

From: Carmen Valladares (cjvalladares_at_ucdavis.edu)
Date: Fri Aug 21 2009 - 16:26:04 CDT

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<javah_at_itn.liu.se?Subject=RE:%20NAMD%20tutorial%20for%20Windows%20problem%20reading%20pgn%20file%20from%20vmd%20tkconsole%20%28fwd%29>>
To: owner-tutorial-l_at_ks.uiuc.edu<owner-tutorial-l_at_ks.uiuc.edu?Subject=RE:%20NAMD%20tutorial%20for%20Windows%20problem%20reading%20pgn%20file%20from%20vmd%20tkconsole%20%28fwd%29>
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<owner-tutorial-l_at_mailhost.ks.uiuc.edu?Subject=RE:%20NAMD%20tutorial%20for%20Windows%20problem%20reading%20pgn%20file%20from%20vmd%20tkconsole%20%28fwd%29>
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