log started: Wed Apr 30 18:07:29 2014 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >>> # using parmbsc0 for nucleic acid. >>> # ----- 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" } >>> { "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" } >>> { "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" "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" } >>> { "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: /usr/local/amber12/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: 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) >>> frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) >>> frcmodbsc0 = loadamberparams frcmod.parmbsc0 Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.parmbsc0 Reading force field modification type file (frcmod) Reading title: modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/ >>> # >>> # Load DNA/RNA libraries >>> # >>> loadOff all_nucleic94.lib Loading library: /usr/local/amber12/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 (i.e. ff94 libs) >>> # >>> loadOff all_amino94.lib Loading library: /usr/local/amber12/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: /usr/local/amber12/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: /usr/local/amber12/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 DNA_CI.lib Loading library: /usr/local/amber12/dat/leap/lib/DNA_CI.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 >>> # >>> # Load water and ions >>> # >>> loadOff ions94.lib Loading library: /usr/local/amber12/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: /usr/local/amber12/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX 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 >>> >>> # >>> # 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" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >>> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >>> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >>> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> >>> } >>> >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'1" } >>> { "H2*2" "H2'2" } >>> { "H2'" "H2'1" } >>> { "H2''" "H2'2" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'1" } >>> { "H5*2" "H5'2" } >>> { "H5'" "H5'1" } >>> { "H5''" "H5'2" } >>> { "HO2'" "HO'2" } >>> { "HO5'" "H5T" } >>> { "HO3'" "H3T" } >>> # old ff atom names -> new >>> { "O1'" "O4'" } >>> { "OA" "O1P" } >>> { "OB" "O2P" } >>> { "OP1" "O1P" } >>> { "OP2" "O2P" } >>> } >>> >>> >>> # >>> # assumed that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> loadoff AMM.lib Loading library: ./AMM.lib Loading: AMM >> loadamberparams NH4.frcmod Loading parameters: ./NH4.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here >> loadamberparams DGP.frcmod Loading parameters: ./DGP.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here >> loadamberprep DGP.prepi Loading Prep file: ./DGP.prepi Loaded UNIT: DGP > > ciao=loadpdb TGpohT_leap.pdb Loading PDB file: ./TGpohT_leap.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue DT, term: Terminal/beginning, seq. number: 0 to: DT5. (Residue 1: DG, Nonterminal, was not found in name map.) (Residue 2: DGP, Nonterminal, was not found in name map.) (Residue 3: DGP, Nonterminal, was not found in name map.) (Residue 4: DGP, Nonterminal, was not found in name map.) Mapped residue DT, term: Terminal/last, seq. number: 5 to: DT3. Mapped residue DT, term: Terminal/beginning, seq. number: 6 to: DT5. (Residue 7: DG, Nonterminal, was not found in name map.) (Residue 8: DGP, Nonterminal, was not found in name map.) (Residue 9: DGP, Nonterminal, was not found in name map.) (Residue 10: DGP, Nonterminal, was not found in name map.) Mapped residue DT, term: Terminal/last, seq. number: 11 to: DT3. Mapped residue DT, term: Terminal/beginning, seq. number: 12 to: DT5. (Residue 13: DG, Nonterminal, was not found in name map.) (Residue 14: DGP, Nonterminal, was not found in name map.) (Residue 15: DGP, Nonterminal, was not found in name map.) (Residue 16: DGP, Nonterminal, was not found in name map.) Mapped residue DT, term: Terminal/last, seq. number: 17 to: DT3. Mapped residue DT, term: Terminal/beginning, seq. number: 18 to: DT5. (Residue 19: DG, Nonterminal, was not found in name map.) (Residue 20: DGP, Nonterminal, was not found in name map.) (Residue 21: DGP, Nonterminal, was not found in name map.) (Residue 22: DGP, Nonterminal, was not found in name map.) Mapped residue DT, term: Terminal/last, seq. number: 23 to: DT3. (Residue 24: AMM, Terminal/last, was not found in name map.) (Residue 25: AMM, Terminal/last, was not found in name map.) (Residue 26: AMM, Terminal/last, was not found in name map.) Joining DT5 - DG Joining DG - DGP Joining DGP - DGP Joining DGP - DGP Joining DGP - DT3 Joining DT5 - DG Joining DG - DGP Joining DGP - DGP Joining DGP - DGP Joining DGP - DT3 Joining DT5 - DG Joining DG - DGP Joining DGP - DGP Joining DGP - DGP Joining DGP - DT3 Joining DT5 - DG Joining DG - DGP Joining DGP - DGP Joining DGP - DGP Joining DGP - DT3 total atoms in file: 807 > check ciao Checking 'ciao'.... WARNING: The unperturbed charge of the unit: -5.000000 is not zero. WARNING: The perturbed charge: -5.000000 is not zero. Warning: Close contact of 1.470319 angstroms between .R.A and .R.A Warning: Close contact of 1.485859 angstroms between .R.A and .R.A

Warning: Close contact of 0.948258 angstroms between .R.A and .R.A Warning: Close contact of 1.450608 angstroms between .R.A and .R.A Warning: Close contact of 0.598841 angstroms between .R.A and .R.A Checking parameters for unit 'ciao'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 7 Unit is OK. > saveamberparm ciao TGpohT.prmtop TGpohT.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -5.000000 is not zero. WARNING: The perturbed charge: -5.000000 is not zero. -- ignoring the warnings. 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 OH-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OH-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-H1 atoms are: O5' H5'1 C5' H5'2 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'1 C5' C4' ** Warning: No sp2 improper torsion term for OS-H1-CI-CT atoms are: O5' H5'2 C5' C4' ** Warning: No sp2 improper torsion term for H1-H1-CI-CT atoms are: H5'1 H5'2 C5' C4' old PREP-specified impropers: : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : C6 C2 N1 H1 : N2 N1 C2 N3 : C2 H21 N2 H22 : C5 N9 C4 N3 total 176 improper torsions applied 96 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 AMM 3 ) (no restraints) > quit Quit