actregiondefine.chm

#############
# ONLY USE IF STARTING NEW SYSTEM AND MISSING ACT 
##############

if { $argv == "" } {
puts "\033\[31mNo fragment file given.\033\[0m Do chemshell.bash regiondefine.chm fragmentfile.c"
exit
}
#Chemshell-script location
set scriptdir /home/ragnarbj/QM-MM/nitrogenase/Chemshell-QM-MM-scripts

#Putting fragment file in memory. 
set frag $argv
fragment $frag old persistent
#Colored output
#puts "Why not \033\[34mGooge\033\[0m first ?"
#puts "Why not \033\[34mG\033\[31mo\033\[33mo\033\[34mg\033\[32ml\033\[31me\033\[0m first ?"

source $scriptdir/procs.tcl
##################################################################
# SETTING UP ACTIVE ATOMS, FROZEN ATOMS AND CONSTRAINTS
##################################################################
source save-new.chm
# Set origin atom (atom in the middle of active region). Here carbon of FeMoco
set origin 17793
#Radius of active region (will select whole residues).
set radius 11
#Freezing special residues/atoms by atom numbers.
#Use seq function select range: Example: set frozgr1 [seq 17730 to 17829]
# or define list explictly: set frozgr1 { 17730 17731 17732 etc} .
# Combine by concat to list $extrafrozen (will be added to $frozen by select.tcl)
# IMIA, FE2P:
set frozgr1 [seq 17730 to 17775 ]
# P-cluster:
set frozgr2 [seq 17794 to 17808]
# These are counterions:
set frozgr3 [seq 37042 to 37066 ]
# These are cysteine sulfur atoms in P-cluster:
set frozgr4 {951 2350 9021 9901 8663 1323}

set extrafrozen [concat $frozgr1 $frozgr2 $frozgr3 $frozgr4 ]
# Calling Tcl code that sets up lists $act and $frozen using $origin, $radius and the frozen lists above.
# act and frozen lists are also written to disk
puts "There are [get_number_of_atoms coords=$frag] atoms."
source $scriptdir/select.tcl

delete_object $frag