VMD-L Mailing List
From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Jun 07 2011 - 04:01:34 CDT
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Dear All,
I have a vmd script (copied below) which I would expect to exit after
finishing, but it does not. Any ideas why? version 1.9, linux, amd64
mol load gro all.gro
source mybigdcd2.tcl
# closewater.tcl
# Justin Gullingsrud
# jgulling_at_mccammon.ucsd.edu
# 8 November 2004
# This script processes a trajectory to create a new file containing just
# a selection of atoms and the N closest water to that selection. The N
# waters are recomputed for each timestep, and need not be the same waters
# in each timestep (in fact, they probably will not be); thus it is in
general
# meaningless to analyze the dynamics of individual waters. However, it
# may be useful for analyzing the distribution of waters around a relatively
# static protein or DNA chain.
# usage: closewater <molid> <selection text> <# waters> <filename prefix>
proc closewater {i} {
set molid 0
set seltext "protein"
set nwat 2500
set prefix "close"
puts "now working in frame $i"
set numinner 0
set inner [list]
set cut 1
while {1} {
set sel [atomselect $molid "name OW and within $cut of ($seltext)"]
set outer [$sel list]
$sel delete
set numouter [llength $outer]
if { $numouter < $nwat } {
set inner $outer
set numinner $numouter
incr cut
continue
}
break
}
puts "Found $numouter waters at cutoff $cut"
catch { unset ohash }
foreach ind $outer { set ohash($ind) 1 }
foreach ind $inner { unset ohash($ind) }
set outer [lrange [array names ohash] 0 [expr $nwat - $numinner - 1]]
set watind [concat $inner $outer]
set sel [atomselect $molid "($seltext) or same residue as (index
$watind)"]
set j [format %06d $i]
$sel writepdb [format $prefix-$j.pdb]
exec editconf -f $prefix-$j.pdb -o $prefix-$j.gro -resnr 1 &
}
bigdcd closewater temp.xtc
bigdcd_wait_till_done
-- Maria G. Technical University of Denmark Copenhagen
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