From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 18 2013 - 02:15:10 CST

On Mon, Feb 18, 2013 at 7:56 AM, Sindrila Dutta Banik
<sindrila_at_iitk.ac.in> wrote:
> Dear all,
>
> I have a trajectory file, which I loaded into VMD. Now want to save the
> coordinates of waters within 10A separation from the substrate. I am able
> to visualize to this using the following command:
>
> waters within 10 of index 6094
>
> but as soon as I am going to save this coordinates for water which are
> with in 10A it writes few coordinate partially means one O and one H not
> the second one. How to save the coordinates completely.

the visualization works exactly the same way. you just didn't notice.

the problem is in your selection text. first you restrict the
selection to all atoms that are heuristically determined to be part of
a water molecule and then you selection those atom(!) that are within
10 angstrom of atom 6094. if you what whole water molecules, you have
to add one more section to the selection and ask for: same fragment as
(water and within 10 of index 6094)

axel.

p.s.: please send my regards to your adviser.

>
> With best regards
> sindrila
>
>
> --
> Sindrila Dutta Banik
> C/O Prof. A. Chandra
> Project Scientist
> Department of Chemistry
> IIT Kanpur
> UP 208016

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.