VMD-L Mailing List

From: Joshua Skootsky (joshua.skootsky_at_gmail.com)
Date: Wed May 07 2014 - 07:22:04 CDT

Try it out in VMD, viewing the different selections using the graphical
interface for the selections.

The two selections are different.

Or look at this console output:

>Main< (Skootsky) 7 % set sel1 [atomselect top "water and oxygen within 10
of protein"]
atomselect1
>Main< (Skootsky) 8 % set sel2 [atomselect top "water within 10 of protein
and oxygen"]
atomselect2
>Main< (Skootsky) 9 % $sel1 num
4
>Main< (Skootsky) 10 % $sel2 num
3

Four isn't three. But the four are four oxygen atoms that lie within 10
Angstroms of any protein atom, and the three are three atoms belonging to
one water molecule within 10 Angstroms of oxygen atoms in my protein.

On Wed, May 7, 2014 at 2:56 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Joshua Skootsky
> *Gesendet:* Dienstag, 6. Mai 2014 20:39
> *An:* Ana Celia Vila Verde
> *Cc:* Ramin Ekhteiari; VMD Mailing List
> *Betreff:* Re: vmd-l: number of water molecules within 5 angstroms of the
> ligand
>
>
>
> water within 10 of protein and oxygen
>
>
>
> is different from
>
>
>
> water and oxygen within 10 of protein
>
>
>
> No it’s in fact the same! Both will return the same number of water oxygen
> atoms. If he wants to also count “half” waters, the “same residue as”
> method would be usable.
>
>
>
> 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
>
>
> ------------------------------
> <http://www.avast.com/>
>
> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus<http://www.avast.com/>Schutz ist aktiv.
>
> 

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