set pdb 1qhj_membrane_QwikMD.pdb
	set file [open $pdb r]
	set line [read -nonewline $file]
	set line [split $line "\n"]
	close $file
	set out [open Minimization_restraints.pdb w+]
	set indexfile [open Minimization_restraints.txt r]
	set vmdindexes [read -nonewline $indexfile]
	close $indexfile
	foreach ind $vmdindexes {
		set index [lsearch -index 1 [lrange $line 0 [expr [llength $line] -2] ] $ind]
		if {$index > -1} {
			set lineauxformat ""
			set lineauxformat [string range [lindex $line $index] 0 59]
			append lineauxformat [format  %+*s 6 1.00]
			append lineauxformat [string range [lindex $line $index] 66 end]
			lset line $index $lineauxformat
		}
	}
	for {set i 0} {$i < [llength $line]} {incr i} {
		puts $out [lindex $line $i]
	}
	close $out
cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
PME on
PMEGridspacing 1
margin 2.5
wrapAll on
wrapWater on
useConstantRatio yes
parameters Retinal_schiff_based_qwikmd.str
############################################################################
#cr
#cr            (C) Copyright 1995-2009 The Board of Trustees of the
#cr                        University of Illinois
#cr                         All Rights Reserved
#cr
############################################################################

############################################################################
# RCS INFORMATION:
#
#       $RCSfile: Minimization.conf,v $
#       $Author: jribeiro $        $Locker:  $             $State: Exp $
#       $Revision: 1.2 $       $Date: 2016/02/10 20:41:44 $
#
############################################################################
##START HERE###
##Simulation Template##
# Simulation conditions
coordinates 1qhj_membrane_QwikMD.pdb
structure 1qhj_membrane_QwikMD.psf

#binCoordinates qwikmdTemp.restart.coor
#binVelocities qwikmdTemp.restart.coor
extendedSystem Minimization.xsc

# Simulation conditions
temperature 0


# Harmonic constraints

constraints on
consref Minimization_restraints.pdb
conskfile Minimization_restraints.pdb
constraintScaling 2
consexp 2
conskcol B


# Output Parameters

binaryoutput no
outputname Minimization
outputenergies 40
outputtiming 40
outputpressure 40
binaryrestart yes
dcdfile Minimization.dcd
dcdfreq 1000
XSTFreq 1000
restartfreq 1000
restartname Minimization.restart


# Thermostat Parameters
langevin on
langevintemp 0
langevinHydrogen    off
langevindamping 1

# Barostat Parameters

usegrouppressure yes
useflexiblecell yes
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 273

# Integrator Parameters

timestep 2
firstTimestep 0
fullElectFrequency 2
nonbondedfreq 1


# Force Field Parameters

paratypecharmm on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
exclude scaled1-4
1-4scaling 1.0
rigidbonds all


#Implicit Solvent Parameters

gbis off
alphaCutoff         14.0
ionConcentration    0.15



# Script

minimize 2000


set file [open Minimization.check w+]
set done 1
if {[file exists Minimization.restart.coor] != 1 || [file exists Minimization.restart.vel] != 1 || [file exists Minimization.restart.xsc] != 1 } {
	 set do 0
}
if {$done == 1} {
	puts $file "DONE"
    flush $file
  close $file
} else {
	puts $file "One or more files filed to be written"
   flush $file
  close $file
}