From: nahren manuel (meetnahren_at_yahoo.com)
Date: Mon Aug 25 2008 - 21:55:40 CDT

Dear VMD users,
I noticed two types of  water mediated Hbond interaction,
 
N(27).....H-O-H(14567).....O=C (ASP 97)
 
N(27).....H-O(14567).....H-O-H(15897).....O=C (ASP 97)
                |
               H
Now i dont know how to select the water molecule that is hboned to N27. So I have to check if my water which is hboned to N27 is also involved in any hbond with Asp 97.I have attached the script for your consideration.
 
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# % $Id: residue_rmsd.tcl,v 1.4 2006/03/06 23:56:46 timisgro Exp $
#selecting water molecules close to resid 304 (ligand) and my acceptor N27 (atom)
#
set closewater [atomselect top "water within 3.5 of resid 304 and name N27"]
#
# selecting N27 atom ; to check hbond between this and closewater
#
set resnameN27 [atomselect top "name N27"]
#selecting resid 97 which is a Asp97 residue
#
set resid97 [atomselect top "resid 97"]
set file1 [open "close8.dat" w]
set n [molinfo top get numframes]
for { set i 1} {$i < $n} {incr i} {
$closewater frame $i
$closewater update
set numwater [$closewater num]
set nhb [llength [lindex [measure hbonds 3.5 60 $closewater $resnameN27] 0]]
set nhbasp97 [llength [lindex [measure hbonds 3.5 60 $closewater $resid97] 0]]
puts $file1 "\n$i\t$numwater \t $nhb $nhbasp97"
puts "$numwater \t $nhb \t $nhbasp97 "
}
close $file1
 
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regards,
nahren