From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 18 2013 - 02:31:13 CST

On Mon, Feb 18, 2013 at 8:46 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com> wrote:
> Try the following
>
> same residue as (waters within 10 of index 6094)

please note that this will only work, if the input data correctly
enumerates residues. this is true for most cases, but not all file
formats do this. using "same fragment" is the safer choice. the same
goes for selection of components in pbcwrap, btw.

axel.

>
> Also, if you look carefully I think the you'll find the atoms missing in the
> visualization as well with your original selection.
>
> Best regards,
>
> Ajasja
>
>
>
>
> On 18 February 2013 07:56, 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.
>>
>> 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.