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: /apps/amber/amber20/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.11, May 2016) > > source leaprc.protein.ff14SB ----- Source: /apps/amber/amber20/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /apps/amber/amber20/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Tue Jan 3 07:44:38 2023 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: /apps/amber/amber20/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /apps/amber/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: /apps/amber/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: /apps/amber/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: /apps/amber/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 leaprc.water.tip3p ----- Source: /apps/amber/amber20/dat/leap/cmd/leaprc.water.tip3p ----- Source of /apps/amber/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: /apps/amber/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: /apps/amber/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: /apps/amber/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: /apps/amber/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: /apps/amber/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: /apps/amber/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) >> > > > set default PBRadii mbondi3 Using ArgH and AspGluO modified Bondi2 radii > > loadamberprep KCX_1.prepin Loading Prep file: ./KCX_1.prepin Loaded UNIT: KCX > loadamberparams KCX_3.frcmod Loading parameters: ./KCX_3.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadamberparams KCX_2.frcmod Loading parameters: ./KCX_2.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > > a = loadPDB 2jff_OK2.pdb Loading PDB file: ./2jff_OK2.pdb -- residue 222: duplicate [ HA] atoms (total 4) -- residue 223: duplicate [ HA] atoms (total 2) -- residue 239: duplicate [ HA] atoms (total 4) /apps/amber/amber20/bin/teLeap: Warning! Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Many instances of duplicate atom names usually come from alternate conformations in the PDB file.) Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. Mapped residue ARG, term: Terminal/last, seq. number: 220 to: CARG. Mapped residue ARG, term: Terminal/beginning, seq. number: 221 to: NARG. Mapped residue GLN, term: Terminal/last, seq. number: 237 to: CGLN. Mapped residue GLU, term: Terminal/beginning, seq. number: 238 to: NGLU. Mapped residue HID, term: Terminal/last, seq. number: 432 to: CHID. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 6494 Leap added 44 missing atoms according to residue templates: 15 Heavy 29 H / lone pairs > > addIons a Na+ 0 15 Na+ ions required to neutralize. Adding 15 counter ions to "a" using 1A grid Total solute charge: -15.00 Max atom radius: 2.00 Grid extends from solute vdw + 3.45 to 9.45 Box: enclosing: -70.37 -31.86 -23.88 15.88 43.99 50.68 sized: 57.63 96.14 104.12 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 3.95% of box, grid points 82890 (no solvent present) Calculating grid charges Placed Na+ in a at (-15.37, -8.86, -8.88). Placed Na+ in a at (-20.37, -0.86, -16.88). Placed Na+ in a at (7.63, 6.14, 11.12). Placed Na+ in a at (-23.37, 19.14, 31.12). Placed Na+ in a at (-50.37, -16.86, 27.12). Placed Na+ in a at (-45.37, 5.14, 43.12). Placed Na+ in a at (-3.37, 16.14, 19.12). Placed Na+ in a at (-13.37, -4.86, -15.88). Placed Na+ in a at (-23.37, -5.86, -3.88). Placed Na+ in a at (-60.37, 11.14, 28.12). Placed Na+ in a at (-1.37, -25.86, 15.12). Placed Na+ in a at (-25.37, 8.14, 38.12). Placed Na+ in a at (4.63, -2.86, 30.12). Placed Na+ in a at (-32.37, 24.14, 18.12). Placed Na+ in a at (-32.37, -11.86, 29.12). Done adding ions. > addIons a Cl- 0 /apps/amber/amber20/bin/teLeap: Warning! addIons: 1st Ion & target unit have charges of the same sign: unit charge = -2e-06; ion1 charge = -1; can't neutralize. > > solvateBox a TIP3PBOX 10 iso Solute vdw bounding box: 74.936 47.561 61.402 Total bounding box for atom centers: 94.936 94.936 94.936 (box expansion for 'iso' is 63.9%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Volume: 941932.484 A^3 Total mass 482832.440 amu, Density 0.851 g/cc Added 24196 residues. > > savepdb a system_leap_3.pdb Writing pdb file: system_leap_3.pdb printing CRYST1 record to PDB file with box info /apps/amber/amber20/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NALA -> ALA /apps/amber/amber20/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CARG -> ARG /apps/amber/amber20/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NARG -> ARG /apps/amber/amber20/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CGLN -> GLN /apps/amber/amber20/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NGLU -> GLU /apps/amber/amber20/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CHID -> HID > > saveamberparm a system_3.top system_3.coord Checking Unit. /apps/amber/amber20/bin/teLeap: Warning! There is a bond of 8.716 angstroms between O3 and C2 atoms: ------- .R.A and .R.A /apps/amber/amber20/bin/teLeap: Warning! There is a bond of 3.202 angstroms between O1 and C4 atoms: ------- .R.A and .R.A /apps/amber/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for O2-CT-C-N atoms are: O3 C1 C2 N old PREP-specified impropers: : -M C1 N1 H1 : C8 C7 N2 H11 : N2 O2 C8 O3 : C1 +M C2 O1 total 1274 improper torsions applied 4 improper torsions in old prep form Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 CGLN 1 CHID 1 NALA 1 NARG 1 NGLU 1 WAT 24196 ) (no restraints) > > quit Quit Exiting LEaP: Errors = 0; Warnings = 10; Notes = 1.