Re: Selecting waters from dynamics trajectory

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 20 2018 - 17:05:43 CDT

Hi Randy,

On Tue, Mar 20, 2018 at 5:47 PM, Randy J. Zauhar <r.zauhar_at_usciences.edu>
wrote:

> Hi wise ones,
>

and wise-body-part ones, too.

>
> I know his has been asked before, but I could not get a coherent answer
> plowing through the thread I found.
>
> I am trying to simply extract all the waters from a trajectory within 5 A
> of my ligand, for every frame. Why does the code below not work?
>

In theory it should, but if the protein drifts significantly, I found it
more convenient to also translate the coordinates. Qwrap does that and the
wrapping symultaneously: https://github.com/jhenin/qwrap

At any rate, I would definitely try the selection through a graphical
representation to make sure.

>
> I have tried this with and without the pbc wrap, same result, have also
> modified the atom selection - I always get a waters that are far away (like
> ~18 A)
>
> Thanks!
>
> Randy
>
> ————————
> mol load psf 5U11_7PS.SWAP.CENTERED.XTALH2O.SOLVATED.IONIZED.psf dcd
> 5U11.SWAP.XTALH2O.RESTRAIN.EQUIL.dcd
> package require pbctools
> pbc wrap -all -compound res -center com -centersel "segname LIG"
>
>
> set fp [ open "activeSiteWaters4.txt" w ]
>
>
> set lastframe [ molinfo top get numframes ]
>
>
> for { set frame 1 } { $frame <= $lastframe } { incr frame 1 } {
>
> set select [ atomselect top "segname WT1 and oxygen within 5. of (segname
> LIG) " frame $frame ]
>

For speed, you could declare the selection outside the loop, and run
$select frame $frame. Also, don't forget $select delete at the end.

> $select update
> set watlist [ $select get {resid name x y z}]
> puts $fp "#$frame"
> foreach water $watlist {
> set resid [ lindex $water 0 ]
> set atom [ lindex $water 1 ]
> set X [ lindex $water 2 ]
> set Y [ lindex $water 3 ]
> set Z [ lindex $water 4 ]
> puts $fp "$resid\t$atom\t$X\t$Y\t$Z"
> }
>
> }
>
> close $fp
> ————————
>
> Randy J. Zauhar, PhD
>
> Prof. of Biochemistry
>
> Dept. of Chemistry & Biochemistry
> University of the Sciences in Philadelphia
> 600 S. 43rd Street
> Philadelphia, PA 19104
>
> Phone: (215)596-8691
> FAX: (215)596-8543
> E-mail: r.zauhar_at_usciences.edu<mailto:r.zauhar_at_usciences.edu>
>
>
>
> “Yeah the night is gonna fall, and the vultures will surround you /
> And when you’re lookin’ in the mirror what you see is gon’ astound you"
>
> — Death Cab for Cutie, “Monday Morning"
>
>
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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