VMD-L Mailing List

From: Ramin Ekhteiari (ramin_ekh_at_REMOVE_yahoo.com)
Date: Mon May 05 2014 - 13:05:21 CDT

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 $fp Out put is : 0 11 1 11 2 11 3 11 4 11 5 11 6 11 7 11 8 11 9 11 10 11 11 11 12 11 13 11 14 11 15 11 16 11 17 11 18 11 19 11 20 11 21 11 22 11 23 11 24 11 25 11 26 11 27 11 28 11 29 11 30 11 . . . On , Ramin Ekhteiari <ramin_ekh_at_yahoo.com> wrote: Dear Norman, I employed this script but it did not change the frames the only it writes the frame No. Cheers, Ramin. set frames [molinfo top get numframes] set fp [open "waters.txt" w] set ligand "protein and resid 37" for {set i 0} {$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> 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.