# Step 1: Create a sphere of proteins lying
#         (In step 2 we will pack lipids around these proteins
#
# ----- Run using: -----
# packmol < step1_proteins.inp
#    (This takes about 30 minutes on an Intel i7 processor)


# ----- Settings:  -----

# All the atoms from diferent proteins will be at least 50.0 Angstrons apart.
tolerance 50.0
# (Setting "discale" to 2.0 increases the typical separation 
#  distance to approximately 2.0*50.0 = 100.0 Angstroms.)
discale 2.0
# The other parameters below are optional:
nloop 10000
maxit 20
seed 12345
sidemax 3000.0
# What fraction of the molecules are moved during "large moves"? (default 0.05)
movefrac 0.05


# The output file name

output step1_proteins.xyz


# File types are in xyz format

filetype xyz



# First, specify the protein inclusions
# We will pack the lipids around these later

structure protein.xyz
  number 120
  atoms 68 69 70
    inside sphere 0. 0. 0. 273.75
  end atoms
  atoms 65 66 67 71 72 73
    outside sphere 0. 0. 0. 325.0
  end atoms
end structure 


