Re: Dowser

From: Basak Isin (isinbasak_at_yahoo.com)
Date: Sat May 29 2010 - 21:48:12 CDT

Hi Hyun,
Thanks for your kind reply.
I changed to csh and source dowserinit and installed dowser. But when I wrote "dowser prot.pdb -probe 0.2 -separation 1.0" to the shell, I still get this error "dowser : command not found". What would be my problem?
Thanks again in advance.
Basak

 Basak Isin

ABOVE ALL NATIONS IS HUMANITY.
"What matters - all that matters, really - is the will to happiness, a kind of enormous, ever-present consciousness. The rest - women, art, success - is nothing but excuses." - Albert Camus

Cause life is meant for living. Yaki-da ;o)

________________________________
From: "Song, Hyundeok (songhk)" <songhk_at_mail.uc.edu>
To: Basak Isin <isinbasak_at_yahoo.com>
Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Sent: Sat, May 29, 2010 9:42:49 PM
Subject: RE: namd-l: Dowser

 
Hi Basak

I think you should run commands at csh instead of bash.
Try this.

# exec csh
# source dowserinit
# dowser

Hyun.
 

________________________________
 
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Basak Isin [isinbasak_at_yahoo.com]
Sent: Saturday, May 29, 2010 8:25 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Dowser

Hi,

I am trying to use Dowser pluggin in VMD to locate water molecules in a protein. In the Dowser website, it is written "before running Dowser execute "source /usr/local/initial/dowserinit".This initalizes the environment variable "DOWSER" and places the Dowser executables in your "path". (The exact location of the file dowserinit depends on the installation.)". I tried doing this. First I downloaded and untarred the Dowser package from their website and tried to source dowserinit but I got the following error.
-bash: setenv: command not found
-bash: setenv: command not found
-bash: dowserinit.txt: line 3: syntax error near unexpected token `('
-bash: dowserinit.txt: line 3: `set path = ( $path $DOWSER/bin $DOWSER/bin/$DOW_MACH )'

dowserinit's content is below:
setenv DOWSER /tmp_mnt/PROGRAMS/DOWSER
setenv DOW_MACH sgi-mips4
set path = ( $path $DOWSER/bin $DOWSER/bin/$DOW_MACH )

I am also away from my linux machine and I am connecting to it using X11 to install Dowser and to open VMD there for using Dowser with it. Because I could not think of a way installing Dowser to my laptop (a windows machine) to use it with VMD.

Thanks in advance for your suggestions...

Have a happy memorial weekend..

Basak

Basak Isin

ABOVE ALL NATIONS IS HUMANITY.
"What matters - all that matters, really - is the will to happiness, a kind of enormous, ever-present consciousness. The rest - women, art, success - is nothing but excuses." - Albert Camus

Cause life is meant for living. Yaki-da ;o)

      

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