VMD-L Mailing List

From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Tue Apr 26 2016 - 18:06:24 CDT

Thank you!

On Tue, Apr 26, 2016 at 6:26 PM, Bennion, Brian <bennion1_at_llnl.gov> wrote:

> the tcl command llength coupled with lsort -unique is what you could use.
> Brian
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Mihaela Drenscko [quo.physics_at_gmail.com]
> *Sent:* Tuesday, April 26, 2016 2:46 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Finding waters near a protein
>
> Hi,
>
> I found this script:
>
> set sel [atomselect top "water and same residue as (within 2 of protein)"]
> set n [molinfo top get numframes]
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> $sel update
> $sel writepdb water_$i.pdb
> }
>
>
> with the output of water atoms near a protein for each frame.
>
> But actually I need to know how many water molecules are near the protein
> , in other words, I need to read into each pdb file, or find other way to
> display the number of water molecule. How can this be accomplished?
>
> Thank you,
> Mihaela
>
> P.S. Or perhaps the number the water molecules can be counted with
> "measure" command? I haven't seen listed a counting results for measuring
> anything. I there an alternative with "measure"?
>
>
>