log started: Wed Mar 3 19:29:46 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the parm99 additive force field, no lone pairs >> # assumes that any unspecified nucleic acids are DNA >> # >> # 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" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "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" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "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" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber9/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber9/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_amino94.lib Loading library: /soft/amber9/dat/leap/lib/all_amino94.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: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff all_aminoct94.lib Loading library: /soft/amber9/dat/leap/lib/all_aminoct94.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: 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 all_aminont94.lib Loading library: /soft/amber9/dat/leap/lib/all_aminont94.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 >> >> loadOff ions94.lib Loading library: /soft/amber9/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 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" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > Sourcing: ./tleap.in > source leaprc.gaff ----- Source: /soft/amber9/dat/leap/cmd/leaprc.gaff ----- Source of /soft/amber9/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Wed Mar 3 19:29:47 2010 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" } >> { "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" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "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" } >> { "pd" "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 gaff.dat Loading parameters: /soft/amber9/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > loadamberprep LIG.prepin Loading Prep file: ./LIG.prepin Loaded UNIT: LIG > loadamberparams LIG.frcmod Loading parameters: ./LIG.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > dlc=loadpdb dlc.pdb Loading PDB file: ./dlc.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: DC5, Terminal/beginning, was not found in name map.) (Residue 1: DG, Nonterminal, was not found in name map.) (Residue 2: DT, Nonterminal, was not found in name map.) (Residue 3: DT, Nonterminal, was not found in name map.) (Residue 4: DT, Nonterminal, was not found in name map.) (Residue 5: DT, Nonterminal, was not found in name map.) (Residue 6: DT, Nonterminal, was not found in name map.) (Residue 7: DT, Nonterminal, was not found in name map.) (Residue 8: DT, Nonterminal, was not found in name map.) (Residue 9: DT, Nonterminal, was not found in name map.) (Residue 10: DT, Nonterminal, was not found in name map.) (Residue 11: DT, Nonterminal, was not found in name map.) (Residue 12: DT, Nonterminal, was not found in name map.) (Residue 13: DT, Nonterminal, was not found in name map.) (Residue 14: DT, Nonterminal, was not found in name map.) (Residue 15: DC3, Terminal/last, was not found in name map.) (Residue 16: DG5, Terminal/beginning, was not found in name map.) (Residue 17: DA, Nonterminal, was not found in name map.) (Residue 18: DA, Nonterminal, was not found in name map.) (Residue 19: DA, Nonterminal, was not found in name map.) (Residue 20: DA, Nonterminal, was not found in name map.) (Residue 21: DA, Nonterminal, was not found in name map.) (Residue 22: DA, Nonterminal, was not found in name map.) (Residue 23: DA, Nonterminal, was not found in name map.) (Residue 24: DA, Nonterminal, was not found in name map.) (Residue 25: DA, Nonterminal, was not found in name map.) (Residue 26: DA, Nonterminal, was not found in name map.) (Residue 27: DA, Nonterminal, was not found in name map.) (Residue 28: DA, Nonterminal, was not found in name map.) (Residue 29: DA, Nonterminal, was not found in name map.) (Residue 30: DC, Nonterminal, was not found in name map.) (Residue 31: DG3, Terminal/last, was not found in name map.) (Residue 32: LIG, Terminal/last, was not found in name map.) Joining DC5 - DG Joining DG - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DT Joining DT - DC3 Joining DG5 - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DA Joining DA - DC Joining DC - DG3 total atoms in file: 784 Leap added 365 missing atoms according to residue templates: 365 H / lone pairs > addions dlc Na+ 0 30 Na+ ions required to neutralize. Adding 30 counter ions to "dlc" using 1A grid Total solute charge: -30.00 Max atom radius: 2.10 Grid extends from solute vdw + 1.87 to 7.97 Box: enclosing: 7.14 2.29 17.75 66.60 69.15 56.27 sized: 135.14 130.29 145.75 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 0 sec Volume = 1.59% of box, grid points 33428 (no solvent present) Calculating grid charges charges: 1 sec Placed Na+ in dlc at (41.14, 47.29, 47.75). Placed Na+ in dlc at (35.14, 33.29, 48.75). Placed Na+ in dlc at (48.14, 34.29, 30.75). Placed Na+ in dlc at (30.14, 44.29, 28.75). Placed Na+ in dlc at (21.14, 26.29, 27.75). Placed Na+ in dlc at (38.14, 59.29, 32.75). Placed Na+ in dlc at (27.14, 35.29, 44.75). Placed Na+ in dlc at (46.14, 47.29, 25.75). Placed Na+ in dlc at (38.14, 24.29, 28.75). Placed Na+ in dlc at (36.14, 19.29, 43.75). Placed Na+ in dlc at (55.14, 46.29, 42.75). Placed Na+ in dlc at (30.14, 45.29, 37.75). Placed Na+ in dlc at (43.14, 30.29, 44.75). Placed Na+ in dlc at (40.14, 61.29, 41.75). Placed Na+ in dlc at (22.14, 34.29, 39.75). Placed Na+ in dlc at (22.14, 20.29, 49.75). Placed Na+ in dlc at (39.14, 30.29, 25.75). Placed Na+ in dlc at (46.14, 38.29, 37.75). Placed Na+ in dlc at (32.14, 38.29, 24.75). Placed Na+ in dlc at (27.14, 17.29, 25.75). Placed Na+ in dlc at (53.14, 50.29, 31.75). Placed Na+ in dlc at (49.14, 47.29, 47.75). Placed Na+ in dlc at (48.14, 24.29, 33.75). Placed Na+ in dlc at (33.14, 52.29, 40.75). Placed Na+ in dlc at (19.14, 31.29, 32.75). Placed Na+ in dlc at (40.14, 48.29, 23.75). Placed Na+ in dlc at (29.14, 19.29, 48.75). Placed Na+ in dlc at (60.14, 48.29, 35.75). Placed Na+ in dlc at (22.14, 29.29, 45.75). Placed Na+ in dlc at (40.14, 20.29, 36.75). Done adding ions. > solvateoct dlc TIP3PBOX 10.0 Scaling up box by a factor of 1.217026 to meet diagonal cut criterion Solute vdw bounding box: 30.553 60.667 27.907 Total bounding box for atom centers: 85.007 85.007 85.007 (box expansion for 'iso' is 152.0%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 318110.444 A^3 (oct) Total mass 172191.032 amu, Density 0.899 g/cc Added 8926 residues. > saveamberparm dlc dlc.prmtop dlc.inpcrd Checking Unit. 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 N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-C-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-C-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC atoms are: N9 C5 C4 N3 ** Warning: No sp2 improper torsion term for NB-C-CB-CB atoms are: N7 C6 C5 C4 old PREP-specified impropers: : C48 C47 N2 C39 : C38 C37 C39 N2 : C39 C36 C38 H29 : C38 C34 C36 H27 : C39 C35 C37 H28 : C37 C34 C35 N12 : C36 C35 C34 N6 : C34 C33 N6 H50 : C25 N6 C33 N12 : C24 C23 C25 C33 : C25 C22 C24 H23 : C24 C20 C22 H21 : C25 C21 C23 H22 : C23 C20 C21 N5 : C21 C19 N5 H49 : C22 C21 C20 N11 : C18 N5 C19 N11 : C17 C16 C18 C19 : C18 C15 C17 H20 : C17 C13 C15 H18 : C18 C14 C16 H19 : C16 C13 C14 H17 : C15 C14 C13 O4 : C9 C8 C7 O1 : C7 C11 C9 H14 : C9 C12 C11 H16 : C7 C10 C8 H13 : C8 C12 C10 H15 : C11 C10 C12 C26 : C12 N7 C26 N10 : C27 C26 N7 H51 : C29 C28 C27 N7 : C31 C27 C29 H24 : C27 C30 C28 N10 : C28 C32 C30 H25 : C31 C30 C32 H26 : C29 C32 C31 C40 : C31 N8 C40 N9 : C42 C40 N8 H52 : C44 C41 C42 N8 : C42 C46 C44 H31 : C44 C45 C46 H32 : C42 C43 C41 N9 : C41 C45 C43 H30 : C46 C43 C45 N3 : C51 C52 N3 C45 total 225 improper torsions applied 46 improper torsions in old prep form Building H-Bond parameters. 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 WAT 8926 ) (no restraints) > quit Quit