VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Mon Nov 08 2004 - 12:51:05 CST

Hi,

Here's a script that might be useful for you and others. You give it
a selection of atoms to search around and a desired number of waters,
and it writes out a series of pdb files containing the selection and
the water molecules closest to the selection, up to that number. You
can then load all the pdb files into VMD and view the trajectory.
It's easiest to load the files from a Unix commmand line with

  vmd mywat-*

assuming "mywat" was the prefix you chose.

Cheers,
Justin

On Mon, 08 Nov 2004 12:18:21 +0100, pl <ladam_at_smbh.univ-paris13.fr> wrote:
> Hi all,
>
> I try to use the bridging_waters.tcl script from Andrew Dalke to display
> waters bridging a DNA during an animation. Although this was written for
> VMD .0, it seems to work, however I have a syntax error message in 1.8.2
> when running calc_bridging:
> ..
> Calculating frame 104 for 0
> syntax error
> Calculating frame 105 for 0
> syntax error
> ..
> this does not seem to preclude functionning of the script as when I
> use 'num_bridging' the results are displayed:
> Frame 0 has 2196 atoms
> Frame 1 has 2212 atoms
> ..
> Though if someone has a clue about this syntax error...
>
> Now I am at the point where I'd like to display bridging waters + DNA
> only (get rid of non bridging H2O) during the animation so that I can
> selectively see waters H-bonded to my DNA.
> This is where I'm stuck, so if someone can help...
>
> Bye all
>
> --
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> | Patrick LADAM | |
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> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"