Re: Dowser

From: Basak Isin (
Date: Sat May 29 2010 - 20:21:38 CDT

Hi Axel,
Thanks for your advice. I will try doing it. Dowser has been a pluggin of VMD for only a couple of years. I remember people using DOWSER without using VMD since at least 2000 to find the location of water molecules in the proteins while preparing the protein for MD simulations. Therefore, people in this group might be more familiar with DOWSER.

From: Axel Kohlmeyer <>
To: Basak Isin <>
Sent: Sat, May 29, 2010 9:09:24 PM
Subject: Re: namd-l: Dowser

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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