VMD-L Mailing List

From: YOLANDA SMALL (yas102_at_psu.edu)
Date: Sun May 15 2005 - 11:39:03 CDT

Hello,

I am running the following script to collect hydrogen bonding info per frame.
However, the scipt will randomly skip frames which meet the hbonding criteria
specified. Any ideas as to why this is happening and how I can fix it?

Thanks,
Yolanda

set nf [molinfo top get numframes]
set sel1 [atomselect top "index 2884 or index 6385"]
puts "Processing $nf frames..."
set cutoff 3.0
set angle 30.0
set abond1 "2884 6385 2889"
set nonbond "{} {} {}"
set chan2 [open 1mut_Tcl_xmgrHB.txt a]
for {set frame 0} {$frame < $nf} {incr frame 1} {
          $sel1 frame $frame
          $sel1 update
          set sel2 [measure hbonds $cutoff $angle $sel1]
          puts $chan1 "h-bonds for frame $frame is $sel2"
          if {$sel2 == $abond1} {puts $chan2 "$frame 1"}
          if {$sel2 == $nonbond} {puts $chan2 "$frame 0"}
}
close $chan2