From: Joshua Skootsky (joshua.skootsky_at_gmail.com)
Date: Tue May 06 2014 - 13:38:46 CDT

water within 10 of protein and oxygen

is different from

water and oxygen within 10 of protein

The first will give you the number of atoms in the water, the second will
give you the number of water molecules.

Your code is current like the first, counting the number of atoms in water
molecules that are within 7 Angstroms of oxygen molecules in your chosen
protein residue.

The relevant line of code should be re-written like this:

set a [atomselect top "(water and oxygen within 7 of ($ligand) )"]

On Tue, May 6, 2014 at 2:35 AM, Ana Celia Vila Verde <acavilaverde_at_gmail.com
> wrote:

> Dear Ramin,
>
> You need to update the selection:
>
> set frames [molinfo top get numframes]
> set fp [open "waters.txt" w]
> set ligand "protein and resid 37"
> for {set i 0} {$i < $frames} {incr i} {
> puts "Frame: $i"
> set a [atomselect top "(water within 7 of ($ligand) and
> oxygen)"]
> $a frame $i
> $a update
> set num [$a num]
> puts $fp "$i $num"
> $a delete
> }
>
> close $fp
>
>
>
> On 5/5/14 8:05 PM, Ramin Ekhteiari wrote:
>
> Dear Norman,
> I employed this script but it did not change the frames the only it writes
> the frame No.
>
>
> Cheers,
> Ramin.
>
> set frames [molinfo top get numframes]
>
> set fp [open "waters.txt" w]
>
> set ligand "protein and resid 37"
>
>
>
> for {set i 0} {$i < $frames} {incr i} {
> puts "Frame: $i"
> set a [atomselect top "(water within 7 of ($ligand) and
> oxygen)"]
> set num [$a num]
> puts $fp "$i $num"
> $a delete
> }
>
> close $fp
> Out put is :
> 0 11
> 1 11
> 2 11
> 3 11
> 4 11
> 5 11
> 6 11
> 7 11
> 8 11
> 9 11
> 10 11
> 11 11
> 12 11
> 13 11
> 14 11
> 15 11
> 16 11
> 17 11
> 18 11
> 19 11
> 20 11
> 21 11
> 22 11
> 23 11
> 24 11
> 25 11
> 26 11
> 27 11
> 28 11
> 29 11
> 30 11
> .
> .
> .
>
> On , Ramin Ekhteiari <ramin_ekh_at_yahoo.com> <ramin_ekh_at_yahoo.com> wrote:
> Dear Norman,
> I employed this script but it did not change the frames the only it writes
> the frame No.
>
>
> Cheers,
> Ramin.
>
> set frames [molinfo top get numframes]
>
> set fp [open "waters.txt" w]
>
> set ligand "protein and resid 37"
>
>
>
> for {set i 0} {$i < $frames} {incr i} {
> puts "Frame: $i"
> set a [atomselect top "(water within 7 of ($ligand) and
> oxygen)"]
> set num [$a num]
> puts $fp "$i $num"
> $a delete
> }
>
> close $fp
> Out put is :
> 0 11
> 1 11
> 2 11
> 3 11
> 4 11
> 5 11
> 6 11
> 7 11
> 8 11
> 9 11
> 10 11
> 11 11
> 12 11
> 13 11
> 14 11
> 15 11
> 16 11
> 17 11
> 18 11
> 19 11
> 20 11
> 21 11
> 22 11
> 23 11
> 24 11
> 25 11
> 26 11
> 27 11
> 28 11
> 29 11
> 30 11
> .
> .
> .
>
> On Monday, May 5, 2014 2:52 PM, Axel Kohlmeyer <akohlmey_at_gmail.com><akohlmey_at_gmail.com>wrote:
> On Mon, May 5, 2014 at 4:47 AM, Ramin Ekhteiari
> <ramin_ekh_at_remove_yahoo.com> wrote:
> > Hi dear all,
> >
> > I would like to calculate number of water molecules within 5 angstroms of
> > the ligand
> > which is bonded to the protein for each step during MD.
> > I tried to do it for one step, but not for all as loop at TCL.
> >
> > So would you please advise me on how to do it.
>
> examples for how to do a loop over all trajectory frames are in the
> user's guide.
>
>
>
> >
> > Would be grateful for any advice.
> >
> >
> > Cheers,
> > Ramin.
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
>
>
>
>

-- 
Joshua Skootsky
(415) 683-9354 | joshua.skootsky_at_gmail.com