-I: Adding /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/prep to search path. -I: Adding /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib to search path. -I: Adding /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm to search path. -I: Adding /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/cmd to search path. -s: Ignoring startup file: leaprc -f: Source build_LK7B_urea.in. Welcome to LEaP! Sourcing: ./build_LK7B_urea.in ----- Source: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/cmd/leaprc.protein.ff14SB done Log file: ./leap.log Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib/amino12.lib Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib/aminoct12.lib Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib/aminont12.lib ----- Source: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/cmd/leaprc.water.tip4pew ----- Source of /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/cmd/leaprc.water.tip4pew done Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib/atomic_ions.lib Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/lib/solvents.lib Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.tip4pew Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP4PEW Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.urea Reading force field modification type file (frcmod) Reading title: Parameters of N - C - N angle and corresponding force const. Loading library: ./URE.off Loading PDB file: ./interface_amber.pdb (starting new molecule for chain B) (starting new molecule for chain A) Created a new atom named: C within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: O within residue: .R Created a new atom named: H1 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H4 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: C within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: O within residue: .R Created a new atom named: H1 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H4 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 4756 Leap added 29 missing atoms according to residue templates: 6 Heavy 23 H / lone pairs The file contained 14 atoms not in residue templates 15 Cl- ions required to neutralize. Adding 15 counter ions to "mol" using 1A grid Used default radius 1.50 for 14 atoms Grid extends from solute vdw + 6.95 to 12.86 Resolution: 1.00 Angstrom. Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Cl- in mol at (-14.38, 15.60, 19.94). (Replacing solvent molecule) Placed Cl- in mol at (-13.03, 21.55, 27.64). (Replacing solvent molecule) Placed Cl- in mol at (-12.40, 30.34, 9.86). (Replacing solvent molecule) Placed Cl- in mol at (-7.53, 26.34, 38.08). (Replacing solvent molecule) Placed Cl- in mol at (-11.69, 14.04, 7.45). (Replacing solvent molecule) Placed Cl- in mol at (-12.86, 4.88, 18.70). (Replacing solvent molecule) Placed Cl- in mol at (-8.49, 37.19, 31.29). (No solvent overlap) Placed Cl- in mol at (1.53, 39.52, 18.29). (Replacing solvent molecule) Placed Cl- in mol at (-10.51, 6.21, 31.10). (Replacing solvent molecule) Placed Cl- in mol at (-15.52, 24.75, 12.10). (No solvent overlap) Placed Cl- in mol at (2.53, -0.48, 20.29). (Replacing solvent molecule) Placed Cl- in mol at (-7.42, 17.32, 38.74). (Replacing solvent molecule) Placed Cl- in mol at (-3.30, 35.43, 7.25). (No solvent overlap) Placed Cl- in mol at (12.53, 16.52, 19.29). (Replacing solvent molecule) Placed Cl- in mol at (-3.12, 2.52, 7.12). Done adding ions. Writing pdb file: interface_tleap.pdb Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/bin/teLeap: Fatal Error! Failed to generate parameters Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0. " "Cu" "sp3" } >> { "Ag+" "Ag" "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" } >> { "OW" "O" "sp3" } >> { "HW" "H" "sp3" } >> { "EP" "" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/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: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/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 = T4E >> WAT = T4E >> loadAmberParams frcmod.tip4pew Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.tip4pew Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP4PEW (UNKNOWN ATOM TYPE: EP) >> loadAmberParams frcmod.ionsjc_tip4pew Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip4pew Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) >> > > > loadamberparams frcmod.urea Loading parameters: /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/dat/leap/parm/frcmod.urea Reading force field modification type file (frcmod) Reading title: Parameters of N - C - N angle and corresponding force const. > loadoff URE.off Loading library: ./URE.off Loading: URE > > mol = loadpdb interface_amber.pdb Loading PDB file: ./interface_amber.pdb (starting new molecule for chain B) (starting new molecule for chain A) Matching PDB residue names to LEaP variables. Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Starting new chain with T4E Created a new atom named: C within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: O within residue: .R Created a new atom named: H1 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H4 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Starting new chain with URE Created a new atom named: C within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: O within residue: .R Created a new atom named: H1 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H4 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 4756 Leap added 29 missing atoms according to residue templates: 6 Heavy 23 H / lone pairs The file contained 14 atoms not in residue templates > addions mol Cl- 0 15 Cl- ions required to neutralize. Adding 15 counter ions to "mol" using 1A grid Used default radius 1.50 for 14 atoms Total solute charge: 15.00 Max atom radius: 1.91 Grid extends from solute vdw + 6.95 to 12.86 Box: enclosing: -30.47 -10.48 -8.71 19.63 47.94 48.55 sized: 33.53 53.52 55.29 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 Volume = 13.80% of box, grid points 36174 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Cl- in mol at (-14.38, 15.60, 19.94). (Replacing solvent molecule) Placed Cl- in mol at (-13.03, 21.55, 27.64). (Replacing solvent molecule) Placed Cl- in mol at (-12.40, 30.34, 9.86). (Replacing solvent molecule) Placed Cl- in mol at (-7.53, 26.34, 38.08). (Replacing solvent molecule) Placed Cl- in mol at (-11.69, 14.04, 7.45). (Replacing solvent molecule) Placed Cl- in mol at (-12.86, 4.88, 18.70). (Replacing solvent molecule) Placed Cl- in mol at (-8.49, 37.19, 31.29). (No solvent overlap) Placed Cl- in mol at (1.53, 39.52, 18.29). (Replacing solvent molecule) Placed Cl- in mol at (-10.51, 6.21, 31.10). (Replacing solvent molecule) Placed Cl- in mol at (-15.52, 24.75, 12.10). (No solvent overlap) Placed Cl- in mol at (2.53, -0.48, 20.29). (Replacing solvent molecule) Placed Cl- in mol at (-7.42, 17.32, 38.74). (Replacing solvent molecule) Placed Cl- in mol at (-3.30, 35.43, 7.25). (No solvent overlap) Placed Cl- in mol at (12.53, 16.52, 19.29). (Replacing solvent molecule) Placed Cl- in mol at (-3.12, 2.52, 7.12). Done adding ions. > > savepdb mol interface_tleap.pdb Writing pdb file: interface_tleap.pdb > saveamberparm mol interface.prmtop interface.inpcrd Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A

does not have a type. /gpfs/loomis/apps/avx/software/Amber/20-foss-2018b/bin/teLeap: Fatal Error! Failed to generate parameters Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.