VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Fri Apr 05 2013 - 05:32:38 CDT

W dniu 04.04.2013 19:54, Yann Fichou pisze:
> Dear all,
>
> I would like to solvate a protein with a define number of water
> molecule. It's unavoidable when one wants a small amount of water
> (typically less than 1 layer).
> I've been through the mailing list and the only answer I found to this
> question is to look into the psfgen tutorial. Which I did, without any
> success.
>
> Could you describe a procedure to do so (if it exists), which I think
> should be useful to appear here?
To my knowledge there is no such feature available directly.
But you might for example adapt the script for solvation in a sphere
available here:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
You could, for example, sort a list of water molecules by distance from
the solute using lsort (http://tmml.sourceforge.net/doc/tcl/lsort.html)
and retain the first N of them.
HTH,
Pawel

>
> Thank you in advance
>
> Yann