VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Thu Apr 06 2006 - 12:09:19 CDT

Hey Jarek,
If you only need to visualize, you could select all water molecules within a
given cutoff of the residue like

water and within 4 of resid 52

and visualize as HBonds.
If it's a trajectory, don't forget to update selection and color every frame
(Graphical Representations -> Trajectory -> Update ...)

If you want to have the water residue numbers, you have to write a script.
Check the "measure hbonds" command in the manual.

Eddi

On Thursday 06 April 2006 15:57, J. Juraszek wrote:
> Hi
> I need to plot water molecules that are h-bonded
> to a protein or a particular protein residue. Is there any way to do this?
> Thank you for any comments.
>
> Jarek
>
> --------------------------------------------------------------
> Jarek Juraszek
> van 't Hoff Institute for Molecular Sciences
> Universit of Amsterdam
> juraszek_at_science.uva.nl
> +31 20 5256492
> -------------------------------------------------------------- 

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Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
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