Re: Dowser

From: Axel Kohlmeyer (
Date: Sat May 29 2010 - 20:09:24 CDT

On Sat, May 29, 2010 at 8:25 PM, Basak Isin <> wrote:
> Hi,

please choose your forum wisely. i.e. questions about VMD are
best posted to the VMD mailing list and not the NAMD list.

> 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 )'

this is obviously c-shell script syntax and you are
obviously running in a bourne shell. of course that
cannot work.

> 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 )

the equivalent script in bourne shell syntax would be:


that should do the trick.


> 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
> "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)

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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