Added bootstrap analysis capabilities and corrected bugs regarding ch…

…ecking of grid boundaries for elastic band algorithm.

examples/amber_vdw.tcl

@@ -0,0 +1,85 @@
+
+# READAMBERVDWARAMS: This routine parses all the AMBER NONBONDED (van der Waals/
+# Lennard-Jones) parameters from a list of AMBER parameter files.
+#
+# Example: read_parm customparams1.par customparams2.par
+
+
+proc read_parm {arg} {
+global typelist rminlist epslist
+
+## Read the file
+  set opened [open "amber_vdw.parms"]
+  set content [read $opened]
+  close $opened
+
+## Split into records on newlines
+  set records [split $content "\n"]
+#  puts Registros_del_archivo	
+#  puts $records	
+#  puts fin_del_archivo	
+
+## Iterate over the records
+   foreach line $records {
+
+#     puts analizando_fila 
+#     puts $line	
+     set list [split $line]
+     set data {}
+     foreach var $list {
+	if {$var != "" } {lappend data $var}
+     }
+     set type [lindex $data 0]
+     set rmin [lindex $data 1]
+     set eps [lindex $data 2]
+
+#     puts $type
+#     puts $rmin
+#     puts $eps
+     lappend typelist $type
+     lappend rminlist $rmin  
+     lappend epslist $eps
+   }
+   puts fin_del_ciclo_sobre_parms
+#   puts $typelist
+#   puts $rminlist
+#   puts $epslist	
+}
+
+
+# ASSIGNAMBEPARMS: This routine sets the beta and occupancy fields of every atom
+# in the specified molecule to what is needed forrunning the implicit ligand sampling 
+# analysis. "read_parms" must have been previously run on the desired parameter 
+# files.
+#
+# Example: assign_vdw 0
+
+proc assign_vdw {molid} {
+global typelist rminlist epslist
+
+#  puts $molid
+  set atomtypes [[atomselect $molid all] get type]
+#  puts Atom_types	
+#  puts $atomtypes 
+
+  set atomradii {}
+  set atomepsilon {}
+
+  foreach tp $atomtypes { 
+      set index [lsearch $typelist $tp]
+      lappend atomradii [lindex $rminlist $index]
+      lappend atomepsilon  [expr {-1 * [lindex $epslist $index]}]
+      if {$index == -1 } {
+      set index 0
+      puts $tp not_found }
+
+  }   		
+
+#  puts $atomradii
+#  puts $atomepsilon  
+  [atomselect $molid all] set radius $atomradii
+  [atomselect $molid all] set occupancy $atomepsilon
+#  [atomselect $molid all] set beta $atomepsilon
+}
+
+