#-----------------------------------------------
# combine several reference structures into one 
#
# variables:
# $(active): mol2 filename
# $(j): infile number
# $(i): loop variable
#
#------------------------------------------------

# read input
TEST_LIG
   READ mol/$(active) all
END

REF_LIG 
   READ mol/$(active) $(j)
   READG $(pfad)/gauss2/$(active)_$(j)_$(i_1) 2 y  
# overwrite old Gaussians with some saved solution
END

#align structures 
TEST_LIG
   SELECT $(molecule)
   SELBAS a f                                      
END

SUPERPOS
   PLACEBAS 3
   COMPLEX
END

# enrich reference structure
TEST_LIG
   WRITEG $(pfad)/tmp/$0/$(active)_$(j)_$(i_1)_superpos 2 1 all    
# save the new gaussians
END

REF_LIG
   READG $(pfad)/tmp/$0/$(active)_$(j)_$(i_1)_superpos 2 n         
# add the extra gaussians
   MERGEG all
# reduce some gaussians, speeding up computation time
   WRITEG $(pfad)/gauss2/$(active)_$(j)_$(i) 2 all
# save enriched gaussians
END