VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Sep 14 2006 - 11:16:21 CDT

Dear all,
    I am trying to find what residues of the protein form Hbonds with
the surrounding lipids. I have the following script that counts the
number of Hbonds. But I do not know how can I change it give me the
resid of the residues from the protein involved.

thanks a lot.
Rgds,
Nitin

set d1 [atomselect $mol "protein"]
set a1 [atomselect $mol "resname POP"]
set d2 [atomselect $mol "resname POP"]
set a2 [atomselect $mol "protein"]
for {set i 0} {$i < 2} {incr i} {
 $d1 frame $i
 $a1 frame $i
 $d2 frame $i
 $a2 frame $i
set nhb1 [llength [lindex [measure hbonds 3.6 60 $d1 $a1] 0]]
set nhb2 [llength [lindex [measure hbonds 3.6 60 $d2 $a2] 0]]
set nhb [expr $nhb1 +$nhb2]
puts "number of h-bonds in frame $i : $nhb"
}