VMD-L Mailing List

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Fri Aug 21 2009 - 17:13:21 CDT

Hi Carmen -

You need to use the tkconsole to change to the correct directory, its
just like the command prompt:

"cd DIRECTORY_NAME"

Instead of "dir" in DOS, the tkconsole uses the unix command "ls" to
list files.

I hope this helps!

-Eric

On Aug 21, 2009, at 5:01 PM, Carmen Valladares wrote:

> Eric,
> You're right I was in a completely different directory. I believed I
> was in the right one because in the Command Prompt window, I typed:
>
> cd C:\Documents and Settings\Dorte\My Documents\CBST Carmen
> Valladares\namd tutorial files\namd-tutorial-files\1-1-build
>
> C:\Documents and Settings\Dorte\My Documents\CBST Carmen Valladares
> \namd tutorial files\namd-tutorial-files\1-1-build>dir
> Volume in drive C has no label.
> Volume Serial Number is 3438-2A90
>
> Directory of C:\Documents and Settings\Dorte\My Documents\CBST
> Carmen Valladares\namd tutorial files\namd-tutorial-files\1-1-build
>
> 08/21/2009 02:05 PM <DIR> .
> 08/21/2009 02:05 PM <DIR> ..
> 10/24/2007 11:09 AM 60,926 1UBQ.pdb
> 08/21/2009 01:09 PM <DIR> example-output
> 10/24/2007 11:09 AM 184,403 top_all27_prot_lipid.inp
> 08/21/2009 02:04 PM 204 ubq.pgn
> 08/21/2009 01:55 PM 8 ubq.PGO
> 08/21/2009 02:04 PM 204 ubq.txt
> 10/24/2007 11:09 AM 2,086 wat_sphere.tcl
> 6 File(s) 247,831 bytes
> 3 Dir(s) 188,715,126,784 bytes free
>
> However, when I typed in the VMD TkConsole the following directory
> came up.
> >Main< (VMD) 14 % pwd
> C:/Program Files/University of Illinois/VMD
>
> How do I ensure I'm in the right directory?
>
> Its cool to hear fellow Aggies are in places you least expect it!
>
> Thank you again.
> ~Carmen
>
>
> On Fri, Aug 21, 2009 at 2:40 PM, Eric H. Lee <ericlee_at_ks.uiuc.edu>
> wrote:
> 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
>