#Loading force fields, etc.
source /usr/local/amber20/dat/leap/cmd/leaprc.gaff2
source /usr/local/amber20/dat/leap/cmd/leaprc.protein.ff14SB
source /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p

#LOADING THE TAIL OF THE SURFACTANT AND CROSS-TERM PARAMETERS
loadamberparams dipeptide_UNA.frcmod
loadamberparams dipeptide_surfactant_tail_head_boundary.frcmod
loadamberprep dipeptide_UNA.prepin
set UNA head null
set UNA tail UNA.1.C1

#CONNECTING THE TAIL TO THE AMINO ACID HEAD GROUPS TO FORM THE INDIVIDUAL SURFACTANT UNITS

#CREATING THE GLYCINE-BASED SURFACTANTS
UGAm = sequence {UNA GLY CALA}
saveoff UGAm UGAm.lib
savemol2 UGAm UGAm.mol2 0
savepdb UGAm UGAm.pdb
set UGAm tail UGAm.1.C10
set UGAm head UGAm.1.C11

UGVm = sequence {UNA GLY CVAL}
saveoff UGVm UGVm.lib
savemol2 UGVm UGVm.mol2 0
savepdb UGVm UGVm.pdb
set UGVm tail UGVm.1.C10
set UGVm head UGVm.1.C11

UGLm = sequence {UNA GLY CLEU}
saveoff UGLm UGLm.lib
savemol2 UGLm UGLm.mol2 0
savepdb UGLm UGLm.pdb
set UGLm tail UGLm.1.C10
set UGLm head UGLm.1.C11

#CREATING THE ALANINE-BASED SURFACTANTS
UAGm = sequence {UNA ALA CGLY}
saveoff UAGm UAGm.lib
savemol2 UAGm UAGm.mol2 0
savepdb UAGm UAGm.pdb
set UAGm tail UAGm.1.C10
set UAGm head UAGm.1.C11

UAAm = sequence {UNA ALA CALA}
saveoff UAAm UAAm.lib
savemol2 UAAm UAAm.mol2 0
savepdb UAAm UAAm.pdb
set UAAm tail UAAm.1.C10
set UAAm head UAAm.1.C11

UAVm = sequence {UNA ALA CVAL}
saveoff UAVm UAVm.lib
savemol2 UAVm UAVm.mol2 0
savepdb UAVm UAVm.pdb
set UAVm tail UAVm.1.C10
set UAVm head UAVm.1.C11

UALm = sequence {UNA ALA CLEU}
saveoff UALm UALm.lib
savemol2 UALm UALm.mol2 0
savepdb UALm UALm.pdb
set UALm tail UALm.1.C10
set UALm head UALm.1.C11

#CREATING THE VALINE-BASED SURFACTANTS
UVGm = sequence {UNA VAL CGLY}
saveoff UVGm UVGm.lib
savemol2 UVGm UVGm.mol2 0
savepdb UVGm UVGm.pdb
set UVGm tail UVGm.1.C10
set UVGm head UVGm.1.C11

UVAm = sequence {UNA VAL CALA}
saveoff UVAm UVAm.lib
savemol2 UVAm UVAm.mol2 0
savepdb UVAm UVAm.pdb
set UVAm tail UVAm.1.C10
set UVAm head UVAm.1.C11

UVVm = sequence {UNA VAL CVAL}
saveoff UVVm UVVm.lib
savemol2 UVVm UVVm.mol2 0
savepdb UVVm UVVm.pdb
set UVVm tail UVVm.1.C10
set UVVm head UVVm.1.C11

UVLm = sequence {UNA VAL CLEU}
saveoff UVLm UVLm.lib
savemol2 UVLm UVLm.mol2 0
savepdb UVLm UVLm.pdb
set UVLm tail UVLm.1.C10
set UVLm head UVLm.1.C11

#CREATING THE LEUCINE-BASED SURFACTANTS
ULGm = sequence {UNA LEU CGLY}
saveoff ULGm ULGm.lib
savemol2 ULGm ULGm.mol2 0
savepdb ULGm ULGm.pdb
set ULGm tail ULGm.1.C10
set ULGm head ULGm.1.C11

ULAm = sequence {UNA LEU CALA}
saveoff ULAm ULAm.lib
savemol2 ULAm ULAm.mol2 0
savepdb ULAm ULAm.pdb
set ULAm tail ULAm.1.C10
set ULAm head ULAm.1.C11

ULVm = sequence {UNA LEU CVAL}
saveoff ULVm ULVm.lib
savemol2 ULVm ULVm.mol2 0
savepdb ULVm ULVm.pdb
set ULVm tail ULVm.1.C10
set ULVm head ULVm.1.C11

ULLm = sequence {UNA LEU CLEU}
saveoff ULLm ULLm.lib
savemol2 ULLm ULLm.mol2 0
savepdb ULLm ULLm.pdb
set ULLm tail ULLm.1.C10
set ULLm head ULLm.1.C11

