log started: Fri Aug 15 12:54:17 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
Loading PDB file: ./b12.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: HIS, 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 - HIE
Joining HIE - 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
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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
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Joining LEU - ASN
Joining ASN - ASN
Joining ASN - PRO
Joining PRO - GLN
Joining GLN - ASP
Joining ASP - PRO
Joining PRO - PHE
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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
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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
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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
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Joining HIE - ARG
Joining ARG - ASP
Joining ASP - PRO
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Joining LYS - TYR
Joining TYR - TRP
Joining TRP - THR
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Joining PRO - GLU
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Joining LYS - PHE
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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 b12_invacuo.topo b12_invacuo.coords
Checking Unit.
WARNING: There is a bond of 4.012864 angstroms between:
------- .R<CYS 415>.A<SG 8> and .R<HEM 473>.A<FE 9>
WARNING: The unperturbed charge of the unit: 3.000400 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for 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 1.334874 to meet diagonal cut criterion
Solute vdw bounding box: 47.633 77.214 63.614
Total bounding box for atom centers: 109.251 109.251 109.251
(box expansion for 'iso' is 56.6%)
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: 670074.437 A^3 (oct)
Total mass 368345.638 amu, Density 0.913 g/cc
Added 17391 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: -40.52 -43.68 -40.28 39.97 40.26 41.40
sized: 87.48 84.32 87.72
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.12% of box, grid points 86306
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 111 sec
(Replacing solvent molecule)
Placed Cl- in aa at (-23.30, -15.13, -4.59).
(Replacing solvent molecule)
Placed Cl- in aa at (-22.60, 16.77, 23.90).
(Replacing solvent molecule)
Placed Cl- in aa at (-7.74, 32.89, 14.02).
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: -39.84 -43.00 -39.60 39.29 40.68 40.72
sized: 88.16 85.00 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.48% of box, grid points 94025
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 99 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-8.90, -26.32, -1.41).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.66, -8.64, -2.30).
(Replacing solvent molecule)
Placed Na+ in aa at (-21.68, -10.77, 2.94).
(Replacing solvent molecule)
Placed Cl- in aa at (-19.47, -17.59, -0.59).
(Replacing solvent molecule)
Placed Na+ in aa at (-21.48, -18.55, 3.76).
(Replacing solvent molecule)
Placed Cl- in aa at (-20.21, -17.96, 7.38).
(Replacing solvent molecule)
Placed Na+ in aa at (-19.93, -12.97, 6.82).
(Replacing solvent molecule)
Placed Cl- in aa at (-24.25, -12.79, 7.05).
(Replacing solvent molecule)
Placed Na+ in aa at (-17.54, -20.15, 11.35).
(Replacing solvent molecule)
Placed Cl- in aa at (-18.60, -24.03, 8.16).
(Replacing solvent molecule)
Placed Na+ in aa at (-17.80, -26.83, 11.94).
(Replacing solvent molecule)
Placed Cl- in aa at (-16.78, -22.96, 14.65).
(Replacing solvent molecule)
Placed Na+ in aa at (-13.42, -20.45, 20.33).
(Replacing solvent molecule)
Placed Cl- in aa at (-13.90, -23.52, 25.11).
(Replacing solvent molecule)
Placed Na+ in aa at (29.76, 0.90, -27.27).
(Replacing solvent molecule)
Placed Cl- in aa at (-14.62, -19.34, 16.55).
(Replacing solvent molecule)
Placed Na+ in aa at (-12.17, -23.82, 16.86).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.01, -16.15, 3.59).
(Replacing solvent molecule)
Placed Na+ in aa at (-19.36, -22.29, 6.18).
(Replacing solvent molecule)
Placed Cl- in aa at (31.57, 0.45, 8.84).
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: -39.84 -43.00 -39.60 39.36 40.68 40.72
sized: 88.16 85.00 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.58% of box, grid points 95983
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 133 sec
(Replacing solvent molecule)
Placed Na+ in aa at (26.85, 9.40, 14.55).
(Replacing solvent molecule)
Placed Cl- in aa at (17.76, -8.06, -22.06).
(Replacing solvent molecule)
Placed Na+ in aa at (20.18, -10.87, -20.67).
(Replacing solvent molecule)
Placed Cl- in aa at (-14.04, -2.20, 25.06).
(Replacing solvent molecule)
Placed Na+ in aa at (-15.55, -2.65, 27.44).
(Replacing solvent molecule)
Placed Cl- in aa at (-20.44, -2.42, 27.25).
(Replacing solvent molecule)
Placed Na+ in aa at (-23.44, 0.83, 29.57).
(Replacing solvent molecule)
Placed Cl- in aa at (-22.78, 3.72, 29.81).
(Replacing solvent molecule)
Placed Na+ in aa at (-21.17, 0.10, 25.86).
(Replacing solvent molecule)
Placed Cl- in aa at (-20.65, 2.39, 27.56).
(Replacing solvent molecule)
Placed Na+ in aa at (-19.77, 6.49, 27.18).
(Replacing solvent molecule)
Placed Cl- in aa at (-22.80, 9.35, 18.04).
(Replacing solvent molecule)
Placed Na+ in aa at (-23.93, 10.77, 14.08).
(Replacing solvent molecule)
Placed Cl- in aa at (-27.62, 7.69, 14.65).
(Replacing solvent molecule)
Placed Na+ in aa at (-24.88, 5.47, 11.78).
(Replacing solvent molecule)
Placed Cl- in aa at (24.28, -8.87, -22.57).
(Replacing solvent molecule)
Placed Na+ in aa at (-30.58, 12.01, 11.86).
(Replacing solvent molecule)
Placed Cl- in aa at (-26.02, 14.43, 12.40).
(Replacing solvent molecule)
Placed Na+ in aa at (-25.25, 5.60, 18.96).
(Replacing solvent molecule)
Placed Cl- in aa at (-25.95, 1.62, 22.86).
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: -39.84 -43.00 -39.60 39.36 40.68 40.72
sized: 88.16 85.00 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.67% of box, grid points 98010
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 128 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-0.32, -25.16, -12.89).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.92, -21.55, -15.92).
(Replacing solvent molecule)
Placed Na+ in aa at (-4.90, -24.26, -17.46).
(Replacing solvent molecule)
Placed Cl- in aa at (-3.57, -26.96, -14.52).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.25, -19.68, -17.99).
(Replacing solvent molecule)
Placed Cl- in aa at (-6.40, -21.87, -20.22).
(Replacing solvent molecule)
Placed Na+ in aa at (-11.72, -21.60, -20.57).
(Replacing solvent molecule)
Placed Cl- in aa at (-13.54, -24.50, -23.85).
(Replacing solvent molecule)
Placed Na+ in aa at (-10.14, -22.73, -22.94).
(Replacing solvent molecule)
Placed Cl- in aa at (-14.76, -24.25, -17.26).
(Replacing solvent molecule)
Placed Na+ in aa at (-14.04, -25.19, -14.77).
(Replacing solvent molecule)
Placed Cl- in aa at (-14.88, -14.85, -18.32).
(Replacing solvent molecule)
Placed Na+ in aa at (-10.80, -15.57, -20.61).
(Replacing solvent molecule)
Placed Cl- in aa at (-9.40, -19.84, -22.84).
(Replacing solvent molecule)
Placed Na+ in aa at (-15.82, -19.67, -17.80).
(Replacing solvent molecule)
Placed Cl- in aa at (-18.65, -21.65, -10.41).
(Replacing solvent molecule)
Placed Na+ in aa at (-18.57, -26.59, -0.86).
(Replacing solvent molecule)
Placed Cl- in aa at (-20.19, -20.96, 2.73).
(Replacing solvent molecule)
Placed Na+ in aa at (-20.76, -26.98, 5.13).
(Replacing solvent molecule)
Placed Cl- in aa at (-15.34, -17.44, -20.60).
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: -39.84 -43.00 -39.60 39.36 40.68 40.72
sized: 88.16 85.00 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.75% of box, grid points 99544
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 130 sec
(No solvent overlap)
Placed Na+ in aa at (4.16, 5.00, -22.60).
(Replacing solvent molecule)
Placed Cl- in aa at (-19.37, -29.34, 2.27).
(Replacing solvent molecule)
Placed Na+ in aa at (-15.13, -30.54, 3.64).
(Replacing solvent molecule)
Placed Cl- in aa at (-16.52, -31.66, 8.28).
(Replacing solvent molecule)
Placed Na+ in aa at (-12.76, -31.07, 11.62).
(Replacing solvent molecule)
Placed Cl- in aa at (-8.05, -30.26, 8.46).
(Replacing solvent molecule)
Placed Na+ in aa at (-8.17, -31.25, 4.67).
(Replacing solvent molecule)
Placed Cl- in aa at (-9.67, -35.62, 2.47).
(Replacing solvent molecule)
Placed Na+ in aa at (-6.96, -34.50, -1.33).
(Replacing solvent molecule)
Placed Cl- in aa at (-11.35, -28.36, 5.83).
(Replacing solvent molecule)
Placed Na+ in aa at (-14.26, -25.83, 7.10).
(Replacing solvent molecule)
Placed Cl- in aa at (-12.97, -30.91, 0.14).
(Replacing solvent molecule)
Placed Na+ in aa at (-15.32, -33.21, -5.51).
(Replacing solvent molecule)
Placed Cl- in aa at (-15.08, -31.70, -3.02).
(Replacing solvent molecule)
Placed Na+ in aa at (-20.88, -31.14, -1.65).
(Replacing solvent molecule)
Placed Cl- in aa at (-10.04, -34.80, 15.60).
(Replacing solvent molecule)
Placed Na+ in aa at (-11.79, -35.13, 0.48).
(Replacing solvent molecule)
Placed Cl- in aa at (-18.43, -33.54, -6.22).
(Replacing solvent molecule)
Placed Na+ in aa at (-17.47, -27.27, -6.30).
(Replacing solvent molecule)
Placed Cl- in aa at (-19.70, -28.03, -3.05).
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: -39.84 -43.41 -39.60 39.36 40.68 40.72
sized: 88.16 84.59 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.82% of box, grid points 101153
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 147 sec
(No solvent overlap)
Placed Na+ in aa at (31.16, 1.59, -9.60).
(Replacing solvent molecule)
Placed Cl- in aa at (6.59, -24.03, -16.30).
(Replacing solvent molecule)
Placed Na+ in aa at (9.08, -22.16, -10.26).
(Replacing solvent molecule)
Placed Cl- in aa at (9.14, -19.62, -13.08).
(Replacing solvent molecule)
Placed Na+ in aa at (5.54, -22.28, -20.11).
(Replacing solvent molecule)
Placed Cl- in aa at (4.21, -19.61, -19.57).
(Replacing solvent molecule)
Placed Na+ in aa at (1.39, -18.93, -20.06).
(Replacing solvent molecule)
Placed Cl- in aa at (12.08, -25.41, -12.58).
(Replacing solvent molecule)
Placed Na+ in aa at (11.60, -21.11, -15.92).
(Replacing solvent molecule)
Placed Cl- in aa at (0.04, -15.63, -21.37).
(Replacing solvent molecule)
Placed Na+ in aa at (1.24, -17.75, -25.85).
(Replacing solvent molecule)
Placed Cl- in aa at (1.17, -20.29, -24.08).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.76, -14.50, -23.53).
(Replacing solvent molecule)
Placed Cl- in aa at (-2.13, -15.58, -26.41).
(Replacing solvent molecule)
Placed Na+ in aa at (-2.88, -19.79, -22.98).
(Replacing solvent molecule)
Placed Cl- in aa at (-3.50, -16.08, -20.02).
(Replacing solvent molecule)
Placed Na+ in aa at (-5.68, -16.33, -18.27).
(Replacing solvent molecule)
Placed Cl- in aa at (-21.68, 9.18, 13.86).
(Replacing solvent molecule)
Placed Na+ in aa at (-16.77, 8.54, 10.46).
(Replacing solvent molecule)
Placed Cl- in aa at (3.72, 23.93, -17.34).
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: -39.84 -43.41 -39.60 39.36 40.68 40.72
sized: 88.16 84.59 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.85% of box, grid points 101608
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 150 sec
(No solvent overlap)
Placed Na+ in aa at (9.16, 13.59, 22.40).
(Replacing solvent molecule)
Placed Cl- in aa at (9.15, -9.28, 10.17).
(Replacing solvent molecule)
Placed Na+ in aa at (4.91, -6.79, 10.46).
(Replacing solvent molecule)
Placed Cl- in aa at (4.31, -7.94, 13.86).
(Replacing solvent molecule)
Placed Na+ in aa at (7.27, -11.63, 12.03).
(Replacing solvent molecule)
Placed Cl- in aa at (4.01, -14.19, 15.03).
(Replacing solvent molecule)
Placed Na+ in aa at (15.95, 10.02, 20.16).
(Replacing solvent molecule)
Placed Cl- in aa at (12.22, 19.39, 19.76).
(Replacing solvent molecule)
Placed Na+ in aa at (13.90, 16.80, 17.71).
(Replacing solvent molecule)
Placed Cl- in aa at (14.09, 12.44, 20.34).
(Replacing solvent molecule)
Placed Na+ in aa at (12.47, 13.18, 22.78).
(Replacing solvent molecule)
Placed Cl- in aa at (11.64, 14.85, 24.90).
(Replacing solvent molecule)
Placed Na+ in aa at (8.09, 16.23, 25.83).
(Replacing solvent molecule)
Placed Cl- in aa at (4.45, 17.67, 26.13).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.00, 19.89, 29.49).
(Replacing solvent molecule)
Placed Cl- in aa at (6.59, -1.04, 23.53).
(Replacing solvent molecule)
Placed Na+ in aa at (4.46, -4.38, 25.11).
(Replacing solvent molecule)
Placed Cl- in aa at (3.83, -7.86, 25.34).
(Replacing solvent molecule)
Placed Na+ in aa at (7.66, -3.04, 16.76).
(Replacing solvent molecule)
Placed Cl- in aa at (8.91, -0.41, 11.62).
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: -39.84 -43.41 -39.60 39.36 40.68 40.72
sized: 88.16 84.59 88.40
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.89% of box, grid points 102455
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 155 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-23.16, -19.55, -2.00).
(Replacing solvent molecule)
Placed Cl- in aa at (10.57, -0.88, 17.15).
(Replacing solvent molecule)
Placed Na+ in aa at (14.85, 1.14, 15.03).
(Replacing solvent molecule)
Placed Cl- in aa at (16.70, 3.32, 22.02).
(Replacing solvent molecule)
Placed Na+ in aa at (20.06, 0.20, 21.96).
(Replacing solvent molecule)
Placed Cl- in aa at (18.47, -0.71, 18.55).
(Replacing solvent molecule)
Placed Na+ in aa at (22.38, 0.26, 16.89).
(Replacing solvent molecule)
Placed Cl- in aa at (25.87, 1.31, 16.06).
(Replacing solvent molecule)
Placed Na+ in aa at (24.87, 1.91, 13.64).
(Replacing solvent molecule)
Placed Cl- in aa at (27.75, -3.37, 12.93).
(Replacing solvent molecule)
Placed Na+ in aa at (25.41, -8.81, 12.37).
(Replacing solvent molecule)
Placed Cl- in aa at (18.93, 1.60, 13.56).
(Replacing solvent molecule)
Placed Na+ in aa at (13.16, 0.70, 19.46).
(Replacing solvent molecule)
Placed Cl- in aa at (26.34, -7.50, 9.88).
(Replacing solvent molecule)
Placed Na+ in aa at (23.62, -3.32, 11.86).
(Replacing solvent molecule)
Placed Cl- in aa at (21.26, -1.26, 10.89).
(Replacing solvent molecule)
Placed Na+ in aa at (30.05, -4.89, 9.79).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.73, -21.76, -21.64).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.18, -24.31, -18.96).
(Replacing solvent molecule)
Placed Cl- in aa at (3.25, -25.88, -19.49).
Done adding ions.
>
> saveamberparm aa b12.topo b12.coords
Checking Unit.
WARNING: There is a bond of 4.012864 angstroms between:
------- .R<CYS 415>.A<SG 8> and .R<HEM 473>.A<FE 9>
-- 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
WAT 17251
)
(no restraints)
>
> quit
Quit
log started: Fri Aug 15 13:18:12 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 b21.pdb
Loading PDB file: ./b21.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: 3874
Leap added 3938 missing atoms according to residue templates:
3908 H / lone pairs
30 unknown element
>
> bond aa.415.SG aa.473.FE
>
> saveamberparm aa b21_invacuo.topo b21_invacuo.coords
Checking Unit.
WARNING: There is a bond of 4.012864 angstroms between:
------- .R<CYS 415>.A<SG 8> and .R<HEM 473>.A<FE 9>
WARNING: The unperturbed charge of the unit: 3.000400 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for 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 1.347013 to meet diagonal cut criterion
Solute vdw bounding box: 49.393 77.185 63.569
Total bounding box for atom centers: 109.513 109.513 109.513
(box expansion for 'iso' is 53.0%)
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: 674854.505 A^3 (oct)
Total mass 370507.558 amu, Density 0.912 g/cc
Added 17511 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: -40.72 -43.36 -41.01 39.81 40.47 40.67
sized: 87.28 84.64 86.99
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.12% of box, grid points 86352
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 118 sec
(Replacing solvent molecule)
Placed Cl- in aa at (-23.00, -15.18, -4.69).
(Replacing solvent molecule)
Placed Cl- in aa at (-1.29, 32.95, 8.37).
(Replacing solvent molecule)
Placed Cl- in aa at (-22.63, 18.58, 21.73).
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: -40.04 -42.68 -40.33 39.13 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.48% of box, grid points 93941
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 124 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-8.60, -26.37, -1.52).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.35, -8.70, -2.40).
(Replacing solvent molecule)
Placed Na+ in aa at (-6.66, -34.55, -1.44).
(Replacing solvent molecule)
Placed Cl- in aa at (-5.88, -30.55, -3.49).
(Replacing solvent molecule)
Placed Na+ in aa at (-2.16, -27.94, -3.59).
(Replacing solvent molecule)
Placed Cl- in aa at (31.87, 0.39, 8.74).
(Replacing solvent molecule)
Placed Na+ in aa at (35.17, 1.53, 6.36).
(Replacing solvent molecule)
Placed Cl- in aa at (9.45, -9.33, 10.06).
(Replacing solvent molecule)
Placed Na+ in aa at (5.21, -6.85, 10.36).
(Replacing solvent molecule)
Placed Cl- in aa at (4.61, -8.00, 13.76).
(Replacing solvent molecule)
Placed Na+ in aa at (2.98, -7.72, 16.05).
(Replacing solvent molecule)
Placed Cl- in aa at (5.42, -5.37, 20.06).
(Replacing solvent molecule)
Placed Na+ in aa at (7.38, -4.90, 9.71).
(Replacing solvent molecule)
Placed Cl- in aa at (9.22, -0.46, 11.51).
(Replacing solvent molecule)
Placed Na+ in aa at (9.55, 2.30, 8.37).
(Replacing solvent molecule)
Placed Cl- in aa at (7.97, -3.09, 16.66).
(Replacing solvent molecule)
Placed Na+ in aa at (8.49, -7.57, 19.15).
(Replacing solvent molecule)
Placed Cl- in aa at (-17.64, -1.20, 25.55).
(Replacing solvent molecule)
Placed Na+ in aa at (-20.35, 2.33, 27.46).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.51, -0.31, 26.59).
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: -40.04 -42.68 -40.33 42.96 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.58% of box, grid points 95964
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 125 sec
(No solvent overlap)
Placed Na+ in aa at (-1.04, -26.68, -12.33).
(Replacing solvent molecule)
Placed Cl- in aa at (-1.39, -24.66, -16.49).
(Replacing solvent molecule)
Placed Na+ in aa at (-4.60, -24.32, -17.57).
(Replacing solvent molecule)
Placed Cl- in aa at (-6.10, -21.92, -20.33).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.43, -21.81, -21.74).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.95, -19.74, -18.09).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.84, -16.93, -19.16).
(Replacing solvent molecule)
Placed Cl- in aa at (1.69, -18.99, -20.17).
(Replacing solvent molecule)
Placed Na+ in aa at (2.97, -15.97, -21.99).
(Replacing solvent molecule)
Placed Cl- in aa at (5.20, -15.36, -25.28).
(Replacing solvent molecule)
Placed Na+ in aa at (6.28, -18.00, -13.86).
(Replacing solvent molecule)
Placed Cl- in aa at (10.04, -19.32, -10.12).
(Replacing solvent molecule)
Placed Na+ in aa at (9.38, -22.22, -10.36).
(Replacing solvent molecule)
Placed Cl- in aa at (7.38, -21.38, -14.23).
(Replacing solvent molecule)
Placed Na+ in aa at (11.90, -21.17, -16.02).
(Replacing solvent molecule)
Placed Cl- in aa at (12.82, -25.58, -16.52).
(Replacing solvent molecule)
Placed Na+ in aa at (13.49, -29.13, -20.20).
(Replacing solvent molecule)
Placed Cl- in aa at (12.31, -28.01, -10.91).
(Replacing solvent molecule)
Placed Na+ in aa at (9.31, -28.04, -16.13).
(Replacing solvent molecule)
Placed Cl- in aa at (13.08, -33.50, -19.18).
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: -40.04 -42.68 -40.33 42.96 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.68% of box, grid points 98160
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 145 sec
(Replacing solvent molecule)
Placed Na+ in aa at (25.52, 12.07, 15.30).
(Replacing solvent molecule)
Placed Cl- in aa at (6.66, -25.60, -18.89).
(Replacing solvent molecule)
Placed Na+ in aa at (8.39, -27.92, -18.76).
(Replacing solvent molecule)
Placed Cl- in aa at (7.10, -30.24, -18.43).
(Replacing solvent molecule)
Placed Na+ in aa at (10.19, -30.27, -17.81).
(Replacing solvent molecule)
Placed Cl- in aa at (25.06, 14.23, 21.33).
(Replacing solvent molecule)
Placed Na+ in aa at (28.48, -1.33, -27.91).
(Replacing solvent molecule)
Placed Cl- in aa at (12.06, -27.04, -21.53).
(Replacing solvent molecule)
Placed Na+ in aa at (13.46, -22.35, -20.47).
(Replacing solvent molecule)
Placed Cl- in aa at (12.61, -18.01, -19.27).
(Replacing solvent molecule)
Placed Na+ in aa at (12.89, -13.03, -19.84).
(Replacing solvent molecule)
Placed Cl- in aa at (13.33, -12.26, -25.25).
(Replacing solvent molecule)
Placed Na+ in aa at (14.68, -26.25, -24.53).
(Replacing solvent molecule)
Placed Cl- in aa at (15.15, -21.91, -24.90).
(Replacing solvent molecule)
Placed Na+ in aa at (11.14, -13.87, -26.07).
(Replacing solvent molecule)
Placed Cl- in aa at (17.69, -30.59, -23.02).
(Replacing solvent molecule)
Placed Na+ in aa at (11.12, -31.24, -23.71).
(Replacing solvent molecule)
Placed Cl- in aa at (8.80, -29.65, -24.64).
(Replacing solvent molecule)
Placed Na+ in aa at (21.21, 16.34, 21.56).
(Replacing solvent molecule)
Placed Cl- in aa at (18.41, 20.87, 18.86).
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: -40.04 -42.68 -40.33 42.96 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.83% of box, grid points 101353
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 154 sec
(No solvent overlap)
Placed Na+ in aa at (9.96, 12.32, 21.67).
(Replacing solvent molecule)
Placed Cl- in aa at (18.06, -8.12, -22.16).
(Replacing solvent molecule)
Placed Na+ in aa at (20.48, -10.92, -20.77).
(Replacing solvent molecule)
Placed Cl- in aa at (33.74, 3.62, 5.02).
(Replacing solvent molecule)
Placed Na+ in aa at (32.86, -0.29, 5.84).
(Replacing solvent molecule)
Placed Cl- in aa at (31.13, -1.67, -3.21).
(Replacing solvent molecule)
Placed Na+ in aa at (29.06, 2.76, -3.57).
(Replacing solvent molecule)
Placed Cl- in aa at (29.79, -4.48, 6.38).
(Replacing solvent molecule)
Placed Na+ in aa at (32.50, -2.22, 0.28).
(Replacing solvent molecule)
Placed Cl- in aa at (35.97, 0.59, -0.96).
(Replacing solvent molecule)
Placed Na+ in aa at (34.57, -5.36, -6.56).
(Replacing solvent molecule)
Placed Cl- in aa at (4.02, 23.87, -17.44).
(Replacing solvent molecule)
Placed Na+ in aa at (5.85, 23.66, -20.22).
(Replacing solvent molecule)
Placed Cl- in aa at (7.57, 28.54, -20.97).
(Replacing solvent molecule)
Placed Na+ in aa at (13.46, 23.64, -20.47).
(Replacing solvent molecule)
Placed Cl- in aa at (16.03, 25.72, -23.04).
(Replacing solvent molecule)
Placed Na+ in aa at (1.69, 27.00, -20.17).
(Replacing solvent molecule)
Placed Cl- in aa at (17.00, 26.26, -17.91).
(Replacing solvent molecule)
Placed Na+ in aa at (10.37, 24.00, -18.27).
(Replacing solvent molecule)
Placed Cl- in aa at (-2.58, 26.14, -23.08).
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: -40.04 -42.68 -40.33 43.76 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume = 4.93% of box, grid points 103449
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 158 sec
(No solvent overlap)
Placed Na+ in aa at (3.96, 5.32, -23.33).
(Replacing solvent molecule)
Placed Cl- in aa at (34.26, -4.57, 3.60).
(Replacing solvent molecule)
Placed Na+ in aa at (34.52, -8.76, 5.66).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.95, 26.25, -18.09).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.43, 24.18, -21.74).
(Replacing solvent molecule)
Placed Cl- in aa at (3.36, 24.41, -22.22).
(Replacing solvent molecule)
Placed Na+ in aa at (1.47, 25.65, -24.18).
(Replacing solvent molecule)
Placed Cl- in aa at (-1.53, 25.62, -29.40).
(Replacing solvent molecule)
Placed Na+ in aa at (0.90, 24.59, -28.82).
(Replacing solvent molecule)
Placed Cl- in aa at (5.67, 21.74, -27.50).
(Replacing solvent molecule)
Placed Na+ in aa at (4.75, 17.62, -27.07).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.43, 22.87, -26.44).
(Replacing solvent molecule)
Placed Na+ in aa at (0.12, 19.59, -20.83).
(Replacing solvent molecule)
Placed Cl- in aa at (-5.16, 16.46, -19.33).
(Replacing solvent molecule)
Placed Na+ in aa at (-6.01, 12.86, -17.76).
(Replacing solvent molecule)
Placed Cl- in aa at (-6.32, 10.99, -19.68).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.03, 14.45, -23.07).
(Replacing solvent molecule)
Placed Cl- in aa at (2.98, 15.27, -23.78).
(Replacing solvent molecule)
Placed Na+ in aa at (-6.04, 19.47, -18.69).
(Replacing solvent molecule)
Placed Cl- in aa at (-3.48, 18.93, -23.38).
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: -40.04 -42.68 -40.33 43.76 40.74 39.99
sized: 87.96 85.32 87.67
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 4.99% of box, grid points 104644
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 156 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-3.11, 24.45, -25.36).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.08, 11.44, -25.70).
(Replacing solvent molecule)
Placed Na+ in aa at (-3.25, 9.29, -27.71).
(Replacing solvent molecule)
Placed Cl- in aa at (-4.04, 9.90, -32.53).
(Replacing solvent molecule)
Placed Na+ in aa at (-3.12, 12.44, -32.83).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.58, 16.67, -33.95).
(Replacing solvent molecule)
Placed Na+ in aa at (-4.20, 20.82, -33.98).
(Replacing solvent molecule)
Placed Cl- in aa at (-6.10, 24.06, -20.33).
(Replacing solvent molecule)
Placed Na+ in aa at (-4.96, 27.23, -20.12).
(Replacing solvent molecule)
Placed Cl- in aa at (2.97, 30.02, -21.99).
(Replacing solvent molecule)
Placed Na+ in aa at (4.90, 34.71, -21.56).
(Replacing solvent molecule)
Placed Cl- in aa at (-1.07, 3.83, -28.06).
(Replacing solvent molecule)
Placed Na+ in aa at (-3.45, 5.69, -30.02).
(Replacing solvent molecule)
Placed Cl- in aa at (-6.80, 14.13, -27.56).
(Replacing solvent molecule)
Placed Na+ in aa at (-4.41, 12.62, -25.77).
(Replacing solvent molecule)
Placed Cl- in aa at (-7.44, 9.85, -25.91).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.62, 1.38, -29.30).
(Replacing solvent molecule)
Placed Cl- in aa at (-2.50, -1.04, -32.81).
(Replacing solvent molecule)
Placed Na+ in aa at (-6.09, 2.29, -27.07).
(Replacing solvent molecule)
Placed Cl- in aa at (-8.91, 3.98, -28.49).
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: -40.04 -42.68 -41.77 43.76 42.50 39.99
sized: 87.96 85.32 86.23
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume = 5.13% of box, grid points 107601
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 162 sec
(Replacing solvent molecule)
Placed Na+ in aa at (31.87, 3.14, -12.90).
(Replacing solvent molecule)
Placed Cl- in aa at (35.81, -0.64, -12.92).
(Replacing solvent molecule)
Placed Na+ in aa at (32.08, -0.13, -13.17).
(Replacing solvent molecule)
Placed Cl- in aa at (9.89, -4.41, 8.46).
(Replacing solvent molecule)
Placed Na+ in aa at (12.53, -3.66, 6.39).
(Replacing solvent molecule)
Placed Cl- in aa at (13.81, -0.64, 4.57).
(Replacing solvent molecule)
Placed Na+ in aa at (35.72, -1.53, -16.82).
(Replacing solvent molecule)
Placed Cl- in aa at (33.41, 1.59, -15.55).
(Replacing solvent molecule)
Placed Na+ in aa at (30.84, -1.03, -15.68).
(Replacing solvent molecule)
Placed Cl- in aa at (32.86, -0.29, -20.71).
(Replacing solvent molecule)
Placed Na+ in aa at (30.48, 1.01, -24.64).
(Replacing solvent molecule)
Placed Cl- in aa at (31.90, 1.38, -29.30).
(Replacing solvent molecule)
Placed Na+ in aa at (31.13, -1.67, -29.76).
(Replacing solvent molecule)
Placed Cl- in aa at (29.25, -4.02, -27.90).
(Replacing solvent molecule)
Placed Na+ in aa at (30.37, -3.27, -24.09).
(Replacing solvent molecule)
Placed Cl- in aa at (33.62, -0.54, -28.31).
(Replacing solvent molecule)
Placed Na+ in aa at (29.06, 2.76, -30.12).
(Replacing solvent molecule)
Placed Cl- in aa at (27.56, 4.24, -33.40).
(Replacing solvent molecule)
Placed Na+ in aa at (18.77, -0.77, -34.66).
(Replacing solvent molecule)
Placed Cl- in aa at (26.86, -4.94, -23.04).
Done adding ions.
>
> saveamberparm aa b21.topo b21.coords
Checking Unit.
WARNING: There is a bond of 4.012864 angstroms between:
------- .R<CYS 415>.A<SG 8> and .R<HEM 473>.A<FE 9>
-- 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
WAT 17371
)
(no restraints)
>
> quit
Quit