log started: Thu Feb 24 15:18:13 2022 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "op" "O" "sp3" } >> { "oq" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cs" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "n5" "N" "sp3" } >> { "n6" "N" "sp3" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff2.dat Loading parameters: /usr/local/amber20/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.11, May 2016) > > source /usr/local/amber20/dat/leap/cmd/leaprc.protein.ff14SB ----- Source: /usr/local/amber20/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /usr/local/amber20/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Feb 24 15:18:13 2022 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/amber20/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /usr/local/amber20/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /usr/local/amber20/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /usr/local/amber20/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /usr/local/amber20/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p ----- Source: /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p ----- Source of /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /usr/local/amber20/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /usr/local/amber20/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /usr/local/amber20/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /usr/local/amber20/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /usr/local/amber20/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /usr/local/amber20/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > > #LOADING THE TAIL OF THE SURFACTANT AND CROSS-TERM PARAMETERS > loadamberparams dipeptide_UNA.frcmod Loading parameters: ./dipeptide_UNA.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadamberparams dipeptide_surfactant_tail_head_boundary.frcmod Loading parameters: ./dipeptide_surfactant_tail_head_boundary.frcmod Reading force field modification type file (frcmod) Reading title: SURFACTANT TAIL-HEAD BOUNDARY PARAMETERS > loadamberprep dipeptide_UNA.prepin Loading Prep file: ./dipeptide_UNA.prepin Loaded UNIT: UNA > 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} Sequence: UNA Sequence: GLY Sequence: CALA > saveoff UGAm UGAm.lib Saving UGAm. Building topology. Building atom parameters. > savemol2 UGAm UGAm.mol2 0 Writing mol2 file: UGAm.mol2 Truncating residue name for PDB format: CALA -> CAL > savepdb UGAm UGAm.pdb Writing pdb file: UGAm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CALA -> ALA > set UGAm tail UGAm.1.C10 > set UGAm head UGAm.1.C11 > > UGVm = sequence {UNA GLY CVAL} Sequence: UNA Sequence: GLY Sequence: CVAL > saveoff UGVm UGVm.lib Saving UGVm. Building topology. Building atom parameters. > savemol2 UGVm UGVm.mol2 0 Writing mol2 file: UGVm.mol2 Truncating residue name for PDB format: CVAL -> CVA > savepdb UGVm UGVm.pdb Writing pdb file: UGVm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CVAL -> VAL > set UGVm tail UGVm.1.C10 > set UGVm head UGVm.1.C11 > > UGLm = sequence {UNA GLY CLEU} Sequence: UNA Sequence: GLY Sequence: CLEU > saveoff UGLm UGLm.lib Saving UGLm. Building topology. Building atom parameters. > savemol2 UGLm UGLm.mol2 0 Writing mol2 file: UGLm.mol2 Truncating residue name for PDB format: CLEU -> CLE > savepdb UGLm UGLm.pdb Writing pdb file: UGLm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CLEU -> LEU > set UGLm tail UGLm.1.C10 > set UGLm head UGLm.1.C11 > > #CREATING THE ALANINE-BASED SURFACTANTS > UAGm = sequence {UNA ALA CGLY} Sequence: UNA Sequence: ALA Sequence: CGLY > saveoff UAGm UAGm.lib Saving UAGm. Building topology. Building atom parameters. > savemol2 UAGm UAGm.mol2 0 Writing mol2 file: UAGm.mol2 Truncating residue name for PDB format: CGLY -> CGL > savepdb UAGm UAGm.pdb Writing pdb file: UAGm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CGLY -> GLY > set UAGm tail UAGm.1.C10 > set UAGm head UAGm.1.C11 > > UAAm = sequence {UNA ALA CALA} Sequence: UNA Sequence: ALA Sequence: CALA > saveoff UAAm UAAm.lib Saving UAAm. Building topology. Building atom parameters. > savemol2 UAAm UAAm.mol2 0 Writing mol2 file: UAAm.mol2 Truncating residue name for PDB format: CALA -> CAL > savepdb UAAm UAAm.pdb Writing pdb file: UAAm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CALA -> ALA > set UAAm tail UAAm.1.C10 > set UAAm head UAAm.1.C11 > > UAVm = sequence {UNA ALA CVAL} Sequence: UNA Sequence: ALA Sequence: CVAL > saveoff UAVm UAVm.lib Saving UAVm. Building topology. Building atom parameters. > savemol2 UAVm UAVm.mol2 0 Writing mol2 file: UAVm.mol2 Truncating residue name for PDB format: CVAL -> CVA > savepdb UAVm UAVm.pdb Writing pdb file: UAVm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CVAL -> VAL > set UAVm tail UAVm.1.C10 > set UAVm head UAVm.1.C11 > > UALm = sequence {UNA ALA CLEU} Sequence: UNA Sequence: ALA Sequence: CLEU > saveoff UALm UALm.lib Saving UALm. Building topology. Building atom parameters. > savemol2 UALm UALm.mol2 0 Writing mol2 file: UALm.mol2 Truncating residue name for PDB format: CLEU -> CLE > savepdb UALm UALm.pdb Writing pdb file: UALm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CLEU -> LEU > set UALm tail UALm.1.C10 > set UALm head UALm.1.C11 > > #CREATING THE VALINE-BASED SURFACTANTS > UVGm = sequence {UNA VAL CGLY} Sequence: UNA Sequence: VAL Sequence: CGLY > saveoff UVGm UVGm.lib Saving UVGm. Building topology. Building atom parameters. > savemol2 UVGm UVGm.mol2 0 Writing mol2 file: UVGm.mol2 Truncating residue name for PDB format: CGLY -> CGL > savepdb UVGm UVGm.pdb Writing pdb file: UVGm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CGLY -> GLY > set UVGm tail UVGm.1.C10 > set UVGm head UVGm.1.C11 > > UVAm = sequence {UNA VAL CALA} Sequence: UNA Sequence: VAL Sequence: CALA > saveoff UVAm UVAm.lib Saving UVAm. Building topology. Building atom parameters. > savemol2 UVAm UVAm.mol2 0 Writing mol2 file: UVAm.mol2 Truncating residue name for PDB format: CALA -> CAL > savepdb UVAm UVAm.pdb Writing pdb file: UVAm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CALA -> ALA > set UVAm tail UVAm.1.C10 > set UVAm head UVAm.1.C11 > > UVVm = sequence {UNA VAL CVAL} Sequence: UNA Sequence: VAL Sequence: CVAL > saveoff UVVm UVVm.lib Saving UVVm. Building topology. Building atom parameters. > savemol2 UVVm UVVm.mol2 0 Writing mol2 file: UVVm.mol2 Truncating residue name for PDB format: CVAL -> CVA > savepdb UVVm UVVm.pdb Writing pdb file: UVVm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CVAL -> VAL > set UVVm tail UVVm.1.C10 > set UVVm head UVVm.1.C11 > > UVLm = sequence {UNA VAL CLEU} Sequence: UNA Sequence: VAL Sequence: CLEU > saveoff UVLm UVLm.lib Saving UVLm. Building topology. Building atom parameters. > savemol2 UVLm UVLm.mol2 0 Writing mol2 file: UVLm.mol2 Truncating residue name for PDB format: CLEU -> CLE > savepdb UVLm UVLm.pdb Writing pdb file: UVLm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CLEU -> LEU > set UVLm tail UVLm.1.C10 > set UVLm head UVLm.1.C11 > > #CREATING THE LEUCINE-BASED SURFACTANTS > ULGm = sequence {UNA LEU CGLY} Sequence: UNA Sequence: LEU Sequence: CGLY > saveoff ULGm ULGm.lib Saving ULGm. Building topology. Building atom parameters. > savemol2 ULGm ULGm.mol2 0 Writing mol2 file: ULGm.mol2 Truncating residue name for PDB format: CGLY -> CGL > savepdb ULGm ULGm.pdb Writing pdb file: ULGm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CGLY -> GLY > set ULGm tail ULGm.1.C10 > set ULGm head ULGm.1.C11 > > ULAm = sequence {UNA LEU CALA} Sequence: UNA Sequence: LEU Sequence: CALA > saveoff ULAm ULAm.lib Saving ULAm. Building topology. Building atom parameters. > savemol2 ULAm ULAm.mol2 0 Writing mol2 file: ULAm.mol2 Truncating residue name for PDB format: CALA -> CAL > savepdb ULAm ULAm.pdb Writing pdb file: ULAm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CALA -> ALA > set ULAm tail ULAm.1.C10 > set ULAm head ULAm.1.C11 > > ULVm = sequence {UNA LEU CVAL} Sequence: UNA Sequence: LEU Sequence: CVAL > saveoff ULVm ULVm.lib Saving ULVm. Building topology. Building atom parameters. > savemol2 ULVm ULVm.mol2 0 Writing mol2 file: ULVm.mol2 Truncating residue name for PDB format: CVAL -> CVA > savepdb ULVm ULVm.pdb Writing pdb file: ULVm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CVAL -> VAL > set ULVm tail ULVm.1.C10 > set ULVm head ULVm.1.C11 > > ULLm = sequence {UNA LEU CLEU} Sequence: UNA Sequence: LEU Sequence: CLEU > saveoff ULLm ULLm.lib Saving ULLm. Building topology. Building atom parameters. > savemol2 ULLm ULLm.mol2 0 Writing mol2 file: ULLm.mol2 Truncating residue name for PDB format: CLEU -> CLE > savepdb ULLm ULLm.pdb Writing pdb file: ULLm.pdb xaLeap: Warning! Converting C-terminal residue name to PDB format: CLEU -> LEU > set ULLm tail ULLm.1.C10 > set ULLm head ULLm.1.C11 > > edit ULVm > ULVp = sequence {ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm} Sequence: UNA Sequence: UNA Sequence: UNA