VMD-L Mailing List

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Wed Jun 22 2011 - 23:55:35 CDT

Hi,
I am trying to calculate the number of water molecules around a protein. I
am using tcl script to do so. I have a small doubt regarding the
'atomselect'.
I am using the following command to select the waters from protein:

* set all [atomselect top "name OH2 and (not within $c of protein) and
(within $k of protein)" ]

* My doubt is : this will select water molecules at a certain distance from
the backbone of the protein or the center of mass of the protein or the
alpha C of the protein residues? What does the keyword "protein" include? Is
it the surface of the protein?

Please guide me regarding this.
Thank you
Divya