From: dipak sanap (
Date: Fri Nov 06 2015 - 03:56:41 CST

Hey all,
I have written a script to find nearest neighbours.It works fine but after
writing some out put, it gives following error. Please help me out with
this error.

can't read "l1": no such variable.


#!/bin/env wish

##Script for n neighbours waters for every SOL oxygen.

proc nb {n sel} {
set l3 {};
set wat_oxy [atomselect top "name OW"];
set nbrs [measure contacts 4.5 $wat_oxy $sel];

set wlist [lindex $nbrs 0];
set qlist [lindex $nbrs 1];

foreach qatom $qlist watom $wlist {
set z [atomselect top "index $watom"];
set wresnum [$z get resid];
set d [measure bond "$watom $qatom"];
lappend l1 [list $wresnum $d];

set l2 [lrange [lsort -index 1 [lsort -unique -index 0 [lsort -index 1
-decreasing $l1]]] 0 [expr $n-1]];

foreach water $l2 {
lappend l3 [lindex $water 0];

return $l3

$wat_oxy delete;
array unset $wat_oxy;
array unset $nbrs;
array unset $n;
$sel delete;
array unset $sel;
array unset wlist;
array unset qlist;
array unset qatom;
array unset watom;
$z delete;
array unset $z;
array unset wresnum;
array unset d;
$l1 delete;
array unset l1;
array unset l2;

set o_file [open "closest-4.txt" w];
set wat_oxy [atomselect top "name OW"];
set total_wat [$wat_oxy num];
puts $o_file "Total number of water oxygens are $total_wat"
set reid [$wat_oxy get resid];

foreach a $reid {
set oxy [atomselect top "resid $a and name OW"];
set id [$oxy get resid];
set neig [nb 4 $oxy];
puts $o_file "The residue id $id has neighbours $neig";

array unset oxy;
array unset id;
array unset neig;

close $o_file