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