VMD-L Mailing List

From: Philipp Schoen1 (SCH_at_zurich.ibm.com)
Date: Tue Jun 05 2007 - 09:30:03 CDT

Dear users
i do the following in order to check the distance of hydrogen bonded atoms:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
proc hbdist {"sel0" "sel1"} {
    set out [open "dist.dat" w]
    set numframes [molinfo 0 get numframes]
     puts "$numframes frames!"
     for {set frame 1} {$frame <= $numframes} {incr frame} {
      $sel0 frame $frame
      $sel0 update
      $sel1 frame $frame
      $sel1 update
      set hbonds [measure hbonds 4.0 35 $sel0 $sel1]
      foreach donor [lindex ${hbonds} 0] acceptor [lindex ${hbonds} 1] {
          set datom [atomselect 0 "index $donor"]
          set aatom [atomselect 0 "index $acceptor"]
          foreach donlist [lindex $donor] acclist [lindex $acceptor] {
            set dist [measure bond [list $donlist $acclist]]
            puts $out "$dist"
          }
      }
      $datom delete
      $aatom delete
      unset donlist
      unset acclist
      unset donor
      unset acceptor
    }
    flush $out
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The output however gives quite large values as you can see below. What is
the clue? Do I miss something? I also tried the script of Vlad
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7974.html and get
similar values. Is it beacuse of PBC?
I need to say that if I do not loop over the frames it seems that the
values are not as big as those given below. For single frames I got values
close the 4.0 as given in the measure hbond command.

Cheers
Philipp

########################################################################
OUPUT
Frame: 1

47.980381012
33.2079467773
22.1528739929
7.2495970726
2.90595459938
18.4597625732
19.9984645844
35.3866729736
32.519241333
4.81217718124
34.2958450317
17.1391372681
28.0478878021
7.1199889183
30.2692966461
28.9558620453
3.51633763313
14.2537736893
10.5998191833
5.94095182419