VMD-L Mailing List

From: YOLANDA SMALL (yas102_at_psu.edu)
Date: Mon May 09 2005 - 16:23:24 CDT

Hello,

I would like to calculate the number of hydrogen bonds within a certain region
of the protein.
What is the syntax to select water molecules within 3.1 Ang of a residue?

I tried the following but it didn't work:

set distance 3.1
set nearby [atomselect top "(resname HOH within $distance of resid 189)"]
set cutoff 3.0
set angle 30.0
set chan [open test_output.log a]
for {set frame 0} {$frame < $nf} {incr frame 1} {
          $sel1 frame $frame
          $sel1 update
          set sel2 [measure hbonds $cutoff $angle $sel1]
          puts $chan "h-bonds for frame $frame is $sel2"
}
close $chan