log started: Fri Aug 15 12:56:14 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # 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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > gaffnew = loadamberparams Tmx_gaff.dat Loading parameters: ./Tmx_gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > frcmod = loadamberparams Tmx_f.frcmod Loading parameters: ./Tmx_f.frcmod Reading force field modification type file (frcmod) Reading title: REMARK 8/6 Modified Junmei frcmod Unknown keyword: REMARK ca- in parameter file. > OHT = loadmol2 FOHT_1_RED_ac.mol2 Loading Mol2 file: ./FOHT_1_RED_ac.mol2 Reading MOLECULE named OHT > > aa = loadpdb b12.pdb Could not open file b12.pdb: not found > > bond aa.415.SG aa.473.FE bond: Argument #1 is type String must be of type: [atom] usage: bond [order] > > saveamberparm aa b12_invacuo.topo b12_invacuo.coords saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > > solvateoct aa TIP3PBOX 12.0 iso solvateOct: Argument #1 is type String must be of type: [unit] usage: solvateOct [aniso] [closeness] > > addions aa Cl- 0 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions aa Na+ 10 Cl- 10 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > > saveamberparm aa b12.topo b12.coords saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > > quit Quit log started: Fri Aug 15 12:56:31 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # 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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/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: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > gaffnew = loadamberparams Tmx_gaff.dat Loading parameters: ./Tmx_gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > frcmod = loadamberparams Tmx_f.frcmod Loading parameters: ./Tmx_f.frcmod Reading force field modification type file (frcmod) Reading title: REMARK 8/6 Modified Junmei frcmod Unknown keyword: REMARK ca- in parameter file. > OHT = loadmol2 FOHT_1_RED_ac.mol2 Loading Mol2 file: ./FOHT_1_RED_ac.mol2 Reading MOLECULE named OHT > > aa = loadpdb b13.pdb Loading PDB file: ./b13.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: LYS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) (Residue 473: OHT, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3896 Leap added 3916 missing atoms according to residue templates: 3886 H / lone pairs 30 unknown element > > bond aa.415.SG aa.473.FE > > saveamberparm aa b13_invacuo.topo b13_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: 3.000400 is not zero. -- ignoring the warning. 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 C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1520 improper torsions applied 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 CTHR 1 HEM 1 NHIE 1 OHT 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.302788 to meet diagonal cut criterion Solute vdw bounding box: 46.864 77.718 63.235 Total bounding box for atom centers: 108.985 108.985 108.985 (box expansion for 'iso' is 60.9%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 665230.202 A^3 (oct) Total mass 365354.982 amu, Density 0.912 g/cc Added 17225 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -40.26 -42.40 -40.91 39.61 41.57 40.79 sized: 87.74 85.60 87.09 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.03% of box, grid points 84430 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 118 sec (Replacing solvent molecule) Placed Cl- in aa at (-22.41, -14.05, -7.10). (Replacing solvent molecule) Placed Cl- in aa at (-3.35, 29.80, 6.72). (Replacing solvent molecule) Placed Cl- in aa at (31.73, 0.34, 9.04). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -41.72 -40.23 39.52 40.89 40.11 sized: 88.42 86.28 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.38% of box, grid points 91925 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 133 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.95, -31.92, -0.71). (Replacing solvent molecule) Placed Cl- in aa at (9.25, -1.62, 21.41). (Replacing solvent molecule) Placed Na+ in aa at (11.92, -4.10, 18.59). (Replacing solvent molecule) Placed Cl- in aa at (14.54, -3.32, 15.60). (Replacing solvent molecule) Placed Na+ in aa at (15.00, 1.03, 15.22). (Replacing solvent molecule) Placed Cl- in aa at (11.36, -4.69, 21.73). (Replacing solvent molecule) Placed Na+ in aa at (14.07, -1.15, 21.63). (Replacing solvent molecule) Placed Cl- in aa at (13.31, 0.59, 19.65). (Replacing solvent molecule) Placed Na+ in aa at (26.03, -4.69, -26.39). (Replacing solvent molecule) Placed Cl- in aa at (21.56, -8.66, -22.49). (Replacing solvent molecule) Placed Na+ in aa at (13.04, 10.31, 22.98). (Replacing solvent molecule) Placed Cl- in aa at (11.26, -20.47, 6.54). (Replacing solvent molecule) Placed Na+ in aa at (9.22, -21.57, 4.14). (Replacing solvent molecule) Placed Cl- in aa at (3.87, -24.55, 3.08). (Replacing solvent molecule) Placed Na+ in aa at (5.52, -24.30, -0.66). (Replacing solvent molecule) Placed Cl- in aa at (9.89, -24.45, 1.28). (Replacing solvent molecule) Placed Na+ in aa at (5.70, -22.39, 6.63). (Replacing solvent molecule) Placed Cl- in aa at (5.45, -24.99, 12.77). (Replacing solvent molecule) Placed Na+ in aa at (5.32, -21.37, 14.74). (Replacing solvent molecule) Placed Cl- in aa at (6.73, -21.48, 9.77). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -41.72 -40.23 39.52 40.89 40.11 sized: 88.42 86.28 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.44% of box, grid points 93009 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 124 sec (Replacing solvent molecule) Placed Na+ in aa at (11.49, -24.90, -0.93). (Replacing solvent molecule) Placed Cl- in aa at (9.74, -27.46, -4.52). (Replacing solvent molecule) Placed Na+ in aa at (10.27, -29.53, -8.17). (Replacing solvent molecule) Placed Cl- in aa at (10.99, -33.87, -10.15). (Replacing solvent molecule) Placed Na+ in aa at (11.00, -36.92, -12.50). (Replacing solvent molecule) Placed Cl- in aa at (9.88, -36.75, -8.32). (Replacing solvent molecule) Placed Na+ in aa at (10.08, -29.33, -2.46). (Replacing solvent molecule) Placed Cl- in aa at (13.16, -37.38, -16.69). (Replacing solvent molecule) Placed Na+ in aa at (-2.31, -27.99, -3.29). (Replacing solvent molecule) Placed Cl- in aa at (-21.94, -10.59, -3.04). (Replacing solvent molecule) Placed Na+ in aa at (-26.50, -12.12, -4.34). (Replacing solvent molecule) Placed Cl- in aa at (-28.05, -9.66, -4.85). (Replacing solvent molecule) Placed Na+ in aa at (-30.86, -7.87, -7.56). (Replacing solvent molecule) Placed Cl- in aa at (-29.31, -4.61, -9.15). (Replacing solvent molecule) Placed Na+ in aa at (-25.62, -0.78, -11.63). (Replacing solvent molecule) Placed Cl- in aa at (-27.41, 2.56, -10.29). (Replacing solvent molecule) Placed Na+ in aa at (-31.20, 2.60, -10.61). (Replacing solvent molecule) Placed Cl- in aa at (7.24, -27.95, -3.27). (Replacing solvent molecule) Placed Na+ in aa at (10.82, -32.08, -5.49). (Replacing solvent molecule) Placed Cl- in aa at (14.15, -30.12, -0.66). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -45.17 -40.23 39.52 40.89 40.11 sized: 88.42 82.83 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.60% of box, grid points 96441 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 142 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.74, -26.43, -1.22). (Replacing solvent molecule) Placed Cl- in aa at (-9.65, -28.38, 1.20). (Replacing solvent molecule) Placed Na+ in aa at (-8.01, -31.36, 4.86). (Replacing solvent molecule) Placed Cl- in aa at (-9.45, -33.19, 0.89). (Replacing solvent molecule) Placed Na+ in aa at (-11.91, -33.18, -2.67). (Replacing solvent molecule) Placed Cl- in aa at (-11.63, -37.99, -4.24). (Replacing solvent molecule) Placed Na+ in aa at (-10.32, -35.35, -4.82). (Replacing solvent molecule) Placed Cl- in aa at (-14.93, -31.81, -2.83). (Replacing solvent molecule) Placed Na+ in aa at (-18.41, -26.70, -0.67). (Replacing solvent molecule) Placed Cl- in aa at (-17.24, -25.46, 6.06). (Replacing solvent molecule) Placed Na+ in aa at (-13.89, -23.81, 5.46). (Replacing solvent molecule) Placed Cl- in aa at (-17.51, -21.97, 1.94). (Replacing solvent molecule) Placed Na+ in aa at (-19.76, -20.73, -0.90). (Replacing solvent molecule) Placed Cl- in aa at (-23.00, -19.66, -1.81). (Replacing solvent molecule) Placed Na+ in aa at (-23.14, -15.24, -4.40). (Replacing solvent molecule) Placed Cl- in aa at (-19.42, -19.14, -6.81). (Replacing solvent molecule) Placed Na+ in aa at (-22.62, -19.38, -9.82). (Replacing solvent molecule) Placed Cl- in aa at (-24.22, -16.95, -10.39). (Replacing solvent molecule) Placed Na+ in aa at (-21.11, -12.94, -12.59). (Replacing solvent molecule) Placed Cl- in aa at (-21.94, -16.69, -15.47). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -45.78 -40.23 39.52 40.89 40.11 sized: 88.42 82.22 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.70% of box, grid points 98590 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 143 sec (No solvent overlap) Placed Na+ in aa at (12.42, 17.22, -5.23). (Replacing solvent molecule) Placed Cl- in aa at (20.73, 18.94, -23.10). (Replacing solvent molecule) Placed Na+ in aa at (20.97, 21.00, -19.67). (Replacing solvent molecule) Placed Cl- in aa at (18.63, 22.17, -21.09). (Replacing solvent molecule) Placed Na+ in aa at (22.54, 23.15, -22.74). (Replacing solvent molecule) Placed Cl- in aa at (23.94, 19.19, -20.08). (Replacing solvent molecule) Placed Na+ in aa at (26.78, 10.22, -23.57). (Replacing solvent molecule) Placed Cl- in aa at (24.51, 14.63, -21.69). (Replacing solvent molecule) Placed Na+ in aa at (24.62, 15.62, -17.90). (Replacing solvent molecule) Placed Cl- in aa at (26.37, 12.81, -17.46). (Replacing solvent molecule) Placed Na+ in aa at (29.11, 13.15, -20.67). (Replacing solvent molecule) Placed Cl- in aa at (30.90, 9.08, -22.41). (Replacing solvent molecule) Placed Na+ in aa at (24.86, 16.56, -23.49). (Replacing solvent molecule) Placed Cl- in aa at (-0.76, 24.32, -15.73). (Replacing solvent molecule) Placed Na+ in aa at (-1.77, 30.14, -14.74). (Replacing solvent molecule) Placed Cl- in aa at (-1.62, 32.08, -9.14). (Replacing solvent molecule) Placed Na+ in aa at (-1.59, 29.04, -5.15). (Replacing solvent molecule) Placed Cl- in aa at (1.83, 28.02, -2.95). (Replacing solvent molecule) Placed Na+ in aa at (4.03, 26.71, -1.14). (Replacing solvent molecule) Placed Cl- in aa at (2.47, 31.25, -6.90). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -45.78 -40.23 39.52 40.89 40.11 sized: 88.42 82.22 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.82% of box, grid points 101000 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 149 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.15, 12.81, 35.64). (Replacing solvent molecule) Placed Cl- in aa at (-5.30, 16.40, 34.07). (Replacing solvent molecule) Placed Na+ in aa at (-0.80, 13.56, 34.87). (Replacing solvent molecule) Placed Cl- in aa at (-2.08, 10.85, 35.55). (Replacing solvent molecule) Placed Na+ in aa at (-2.42, 17.76, 33.80). (Replacing solvent molecule) Placed Cl- in aa at (1.91, 17.58, 33.56). (Replacing solvent molecule) Placed Na+ in aa at (-0.27, 13.96, 37.63). (Replacing solvent molecule) Placed Cl- in aa at (-4.70, 12.61, 39.54). (Replacing solvent molecule) Placed Na+ in aa at (-1.59, 6.04, 34.68). (Replacing solvent molecule) Placed Cl- in aa at (2.47, 8.26, 32.92). (Replacing solvent molecule) Placed Na+ in aa at (5.04, 10.34, 30.35). (Replacing solvent molecule) Placed Cl- in aa at (-4.09, 6.52, 37.00). (Replacing solvent molecule) Placed Na+ in aa at (-7.53, 8.20, 39.16). (Replacing solvent molecule) Placed Cl- in aa at (27.97, 12.56, -25.48). (Replacing solvent molecule) Placed Na+ in aa at (24.93, 9.79, -25.61). (Replacing solvent molecule) Placed Cl- in aa at (22.43, 9.20, -28.53). (Replacing solvent molecule) Placed Na+ in aa at (19.86, 6.58, -28.66). (Replacing solvent molecule) Placed Cl- in aa at (-20.72, 14.74, 25.09). (Replacing solvent molecule) Placed Na+ in aa at (-21.84, 13.06, 27.13). (Replacing solvent molecule) Placed Cl- in aa at (-23.87, 16.28, 28.76). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -45.78 -40.23 39.52 40.89 47.33 sized: 88.42 82.22 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.96% of box, grid points 104103 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 152 sec (Replacing solvent molecule) Placed Na+ in aa at (32.16, 9.85, -7.25). (Replacing solvent molecule) Placed Cl- in aa at (36.89, 3.27, -6.11). (Replacing solvent molecule) Placed Na+ in aa at (34.06, 3.95, -6.60). (Replacing solvent molecule) Placed Cl- in aa at (32.30, 7.74, -3.67). (Replacing solvent molecule) Placed Na+ in aa at (30.75, 7.15, -1.47). (Replacing solvent molecule) Placed Cl- in aa at (29.16, 9.51, 1.86). (Replacing solvent molecule) Placed Na+ in aa at (29.11, 13.15, 5.88). (Replacing solvent molecule) Placed Cl- in aa at (30.10, 17.76, 7.25). (Replacing solvent molecule) Placed Na+ in aa at (23.75, 21.71, 0.82). (Replacing solvent molecule) Placed Cl- in aa at (25.03, 24.79, 0.56). (Replacing solvent molecule) Placed Na+ in aa at (26.44, 19.33, 5.28). (Replacing solvent molecule) Placed Cl- in aa at (24.86, 16.56, 3.06). (No solvent overlap) Placed Na+ in aa at (21.42, 16.22, 4.77). (Replacing solvent molecule) Placed Cl- in aa at (24.62, 15.62, 8.65). (Replacing solvent molecule) Placed Na+ in aa at (27.39, 15.14, 10.27). (Replacing solvent molecule) Placed Cl- in aa at (25.84, 16.36, 15.22). (Replacing solvent molecule) Placed Na+ in aa at (24.15, 15.92, 19.65). (Replacing solvent molecule) Placed Cl- in aa at (20.06, 16.75, 17.41). (Replacing solvent molecule) Placed Na+ in aa at (19.37, 25.66, 9.98). (Replacing solvent molecule) Placed Cl- in aa at (20.82, 27.85, 7.52). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.58 -45.78 -40.23 44.68 40.89 47.33 sized: 88.42 82.22 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.09% of box, grid points 106740 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 155 sec (Replacing solvent molecule) Placed Na+ in aa at (27.00, 9.29, 14.74). (Replacing solvent molecule) Placed Cl- in aa at (27.82, 12.61, 12.99). (Replacing solvent molecule) Placed Na+ in aa at (29.93, 16.82, 13.75). (Replacing solvent molecule) Placed Cl- in aa at (32.25, 13.96, 11.08). (Replacing solvent molecule) Placed Na+ in aa at (30.98, 10.93, 13.67). (Replacing solvent molecule) Placed Cl- in aa at (30.55, 7.30, 13.61). (Replacing solvent molecule) Placed Na+ in aa at (19.91, 14.81, 11.81). (Replacing solvent molecule) Placed Cl- in aa at (15.13, 25.72, 11.54). (Replacing solvent molecule) Placed Na+ in aa at (16.86, 26.20, 8.94). (Replacing solvent molecule) Placed Cl- in aa at (6.10, -9.04, 9.28). (Replacing solvent molecule) Placed Na+ in aa at (8.24, -6.87, 12.75). (Replacing solvent molecule) Placed Cl- in aa at (8.65, -6.71, 15.48). (Replacing solvent molecule) Placed Na+ in aa at (6.49, -9.89, 19.41). (Replacing solvent molecule) Placed Cl- in aa at (5.04, -12.66, 17.08). (Replacing solvent molecule) Placed Na+ in aa at (4.16, -14.30, 15.22). (Replacing solvent molecule) Placed Cl- in aa at (3.27, -19.03, 12.60). (Replacing solvent molecule) Placed Na+ in aa at (2.14, -20.47, 10.41). (Replacing solvent molecule) Placed Cl- in aa at (3.23, -16.48, 21.63). (Replacing solvent molecule) Placed Na+ in aa at (0.52, -20.02, 21.73). (Replacing solvent molecule) Placed Cl- in aa at (14.98, -14.89, 9.76). Done adding ions. > > saveamberparm aa b13.topo b13.coords 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 C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1520 improper torsions applied 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 CTHR 1 HEM 1 NHIE 1 OHT 1 WAT 17084 ) (no restraints) > > quit Quit