#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 ULVm SURFACTANT

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

#SAVING FILES FOR UNSOLAVTED ULVm SURFACTANT

saveamberparm ULVm ULVm_unsolvated.prmtop ULVm_unsolvated.inpcrd
saveoff ULVm ULVm_unsolvated.lib
savepdb ULVm ULVm_unsolvated.pdb
savemol2 ULVm ULVm_unsolvated.mol2 0

#SOLVATING ULVm SURFACTANT

solvateOct ULVm TIP3PBOX 10.0
addIons ULVm Na+ 0

#SAVING FILES FOR SOLVATED ULVm SURFACTANT

saveamberparm ULVm ULVm_solvated.prmtop ULVm_solvated.inpcrd
saveoff ULVm ULVm_solvated.lib
savepdb ULVm ULVm_solvated.pdb
savemol2 ULVm ULVm_solvated.mol2 0

quit







