RE: Dowser

From: Song, Hyundeok (songhk) (
Date: Sat May 29 2010 - 20:42:49 CDT

Hi Basak

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

# exec csh
# source dowserinit
# dowser


From: [] on behalf of Basak Isin []
Sent: Saturday, May 29, 2010 8:25 PM
Subject: namd-l: Dowser


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 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 Isin

"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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