#!/usr/bin/tclsh
# this tiny script removes the irritating bond between H1 
# and H2 that VMD inherits when loading Amber topologies
# (it is correct for the operation of Amber, but not
# useful for visualizations).
# Warning: this scripts assumes certain naming conventions
# and ordering that are typical for amber, but may not
# apply in your case. please check carefully.
# 
# (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

# get current bond info

proc fixamberwater {{molid top}} {
    set wat [atomselect $molid water]
    set blist [$wat getbonds]
    set nlist {}

# process the list and remove the bond info 
# (it is the last in the hydrogen bond list).
    foreach {o h1 h2} $blist {
        lappend nlist $o
        lappend nlist [lreplace $h1 1 1]
        lappend nlist [lreplace $h2 1 1]
    }

# override the bonds with the new info
    $wat setbonds $nlist

    $wat delete
}