[senthil@craycx1 test3]$ ./run1.sh -I: Adding /home/tripos/amber11_install/amber11/dat/leap/prep to search path. -I: Adding /home/tripos/amber11_install/amber11/dat/leap/lib to search path. -I: Adding /home/tripos/amber11_install/amber11/dat/leap/parm to search path. -I: Adding /home/tripos/amber11_install/amber11/dat/leap/cmd to search path. -f: Source t1A.in. Welcome to LEaP! Sourcing leaprc: /home/tripos/amber11_install/amber11/dat/leap/cmd/leaprc Log file: ./leap.log Loading parameters: /home/tripos/amber11_install/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/tripos/amber11_install/amber11/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_nucleic94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_amino94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_aminoct94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_aminont94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/ions94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/solvents.lib Sourcing: ./t1A.in ----- Source: /home/tripos/amber11_install/amber11/dat/leap/cmd/leaprc ----- Source of /home/tripos/amber11_install/amber11/dat/leap/cmd/leaprc done Log file: ./leap.log Loading parameters: /home/tripos/amber11_install/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/tripos/amber11_install/amber11/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_nucleic94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_amino94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_aminoct94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/all_aminont94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/ions94.lib Loading library: /home/tripos/amber11_install/amber11/dat/leap/lib/solvents.lib Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT Substituting map 0G -> RG5 for 0G -> RG5 Substituting map 1G -> RG3 for 1G -> RG3 Substituting map G -> RG for G -> RG Substituting map GN -> RGN for GN -> RGN Substituting map 0A -> RA5 for 0A -> RA5 Substituting map 1A -> RA3 for 1A -> RA3 Substituting map A -> RA for A -> RA Substituting map AN -> RAN for AN -> RAN Substituting map 0C -> RC5 for 0C -> RC5 Substituting map 1C -> RC3 for 1C -> RC3 Substituting map C -> RC for C -> RC Substituting map CN -> RCN for CN -> RCN Substituting map 0U -> RU5 for 0U -> RU5 Substituting map 1U -> RU3 for 1U -> RU3 Substituting map U -> RU for U -> RU Substituting map UN -> RUN for UN -> RUN Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map O2* -> O2' for O2* -> O2' Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2'1 for H2*1 -> H2'1 Substituting map H2*2 -> H2'2 for H2*2 -> H2'2 Substituting map H2' -> H2'1 for H2' -> H2'1 Substituting map H2'' -> H2'2 for H2'' -> H2'2 Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5'1 for H5*1 -> H5'1 Substituting map H5*2 -> H5'2 for H5*2 -> H5'2 Substituting map H5' -> H5'1 for H5' -> H5'1 Substituting map H5'' -> H5'2 for H5'' -> H5'2 Substituting map HO2' -> HO'2 for HO2' -> HO'2 Substituting map HO5' -> H5T for HO5' -> H5T Substituting map HO3' -> H3T for HO3' -> H3T Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> O1P for OA -> O1P Substituting map OB -> O2P for OB -> O2P Substituting map OP1 -> O1P for OP1 -> O1P Substituting map OP2 -> O2P for OP2 -> O2P ----- Source: /home/tripos/amber11_install/amber11/dat/leap/cmd/leaprc.gaff ----- Source of /home/tripos/amber11_install/amber11/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /home/tripos/amber11_install/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end Loading parameters: ./myr.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here Loading library: ./myr.lib Loading PDB file: ./pdb1h9z.pdb Created a new atom named: H57 within residue: .R Created a new atom named: H56 within residue: .R Created a new atom named: H55 within residue: .R Created a new atom named: H54 within residue: .R Created a new atom named: H53 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H50 within residue: .R Created a new atom named: H49 within residue: .R Created a new atom named: H48 within residue: .R Created a new atom named: H47 within residue: .R Created a new atom named: H46 within residue: .R Created a new atom named: H45 within residue: .R Created a new atom named: H44 within residue: .R Created a new atom named: H43 within residue: .R Created a new atom named: H42 within residue: .R Created a new atom named: H41 within residue: .R Created a new atom named: H40 within residue: .R Created a new atom named: H39 within residue: .R Created a new atom named: H38 within residue: .R Created a new atom named: H37 within residue: .R Created a new atom named: H36 within residue: .R Created a new atom named: H35 within residue: .R Created a new atom named: H34 within residue: .R Created a new atom named: H33 within residue: .R Created a new atom named: H32 within residue: .R Created a new atom named: H31 within residue: .R Created a new atom named: H84 within residue: .R Created a new atom named: H83 within residue: .R Created a new atom named: H82 within residue: .R Created a new atom named: H81 within residue: .R Created a new atom named: H80 within residue: .R Created a new atom named: H79 within residue: .R Created a new atom named: H78 within residue: .R Created a new atom named: H77 within residue: .R Created a new atom named: H76 within residue: .R Created a new atom named: H75 within residue: .R Created a new atom named: H74 within residue: .R Created a new atom named: H73 within residue: .R Created a new atom named: H72 within residue: .R Created a new atom named: H71 within residue: .R Created a new atom named: H70 within residue: .R Created a new atom named: H69 within residue: .R Created a new atom named: H68 within residue: .R Created a new atom named: H67 within residue: .R Created a new atom named: H66 within residue: .R Created a new atom named: H65 within residue: .R Created a new atom named: H64 within residue: .R Created a new atom named: H63 within residue: .R Created a new atom named: H62 within residue: .R Created a new atom named: H61 within residue: .R Created a new atom named: H60 within residue: .R Created a new atom named: H59 within residue: .R Created a new atom named: H58 within residue: .R Created a new atom named: H111 within residue: .R Created a new atom named: H110 within residue: .R Created a new atom named: H109 within residue: .R Created a new atom named: H108 within residue: .R Created a new atom named: H107 within residue: .R Created a new atom named: H106 within residue: .R Created a new atom named: H105 within residue: .R Created a new atom named: H104 within residue: .R Created a new atom named: H103 within residue: .R Created a new atom named: H102 within residue: .R Created a new atom named: H101 within residue: .R Created a new atom named: H100 within residue: .R Created a new atom named: H99 within residue: .R Created a new atom named: H98 within residue: .R Created a new atom named: H97 within residue: .R Created a new atom named: H96 within residue: .R Created a new atom named: H95 within residue: .R Created a new atom named: H94 within residue: .R Created a new atom named: H93 within residue: .R Created a new atom named: H92 within residue: .R Created a new atom named: H91 within residue: .R Created a new atom named: H90 within residue: .R Created a new atom named: H89 within residue: .R Created a new atom named: H88 within residue: .R Created a new atom named: H87 within residue: .R Created a new atom named: H86 within residue: .R Created a new atom named: H85 within residue: .R Created a new atom named: H138 within residue: .R Created a new atom named: H137 within residue: .R Created a new atom named: H136 within residue: .R Created a new atom named: H135 within residue: .R Created a new atom named: H134 within residue: .R Created a new atom named: H133 within residue: .R Created a new atom named: H132 within residue: .R Created a new atom named: H131 within residue: .R Created a new atom named: H130 within residue: .R Created a new atom named: H129 within residue: .R Created a new atom named: H128 within residue: .R Created a new atom named: H127 within residue: .R Created a new atom named: H126 within residue: .R Created a new atom named: H125 within residue: .R Created a new atom named: H124 within residue: .R Created a new atom named: H123 within residue: .R Created a new atom named: H122 within residue: .R Created a new atom named: H121 within residue: .R Created a new atom named: H120 within residue: .R Created a new atom named: H119 within residue: .R Created a new atom named: H118 within residue: .R Created a new atom named: H117 within residue: .R Created a new atom named: H116 within residue: .R Created a new atom named: H115 within residue: .R Created a new atom named: H114 within residue: .R Created a new atom named: H113 within residue: .R Created a new atom named: H112 within residue: .R Created a new atom named: H165 within residue: .R Created a new atom named: H164 within residue: .R Created a new atom named: H163 within residue: .R Created a new atom named: H162 within residue: .R Created a new atom named: H161 within residue: .R Created a new atom named: H160 within residue: .R Created a new atom named: H159 within residue: .R Created a new atom named: H158 within residue: .R Created a new atom named: H157 within residue: .R Created a new atom named: H156 within residue: .R Created a new atom named: H155 within residue: .R Created a new atom named: H154 within residue: .R Created a new atom named: H153 within residue: .R Created a new atom named: H152 within residue: .R Created a new atom named: H151 within residue: .R Created a new atom named: H150 within residue: .R Created a new atom named: H149 within residue: .R Created a new atom named: H148 within residue: .R Created a new atom named: H147 within residue: .R Created a new atom named: H146 within residue: .R Created a new atom named: H145 within residue: .R Created a new atom named: H144 within residue: .R Created a new atom named: H143 within residue: .R Created a new atom named: H142 within residue: .R Created a new atom named: H141 within residue: .R Created a new atom named: H140 within residue: .R Created a new atom named: H139 within residue: .R total atoms in file: 9453 Leap added 135 missing atoms according to residue templates: 135 H / lone pairs The file contained 135 atoms not in residue templates Since added/missing = extra, there is a high probability of atoms with 'incorrect' names; you may want to use addPdbAtomMap to map these names, or change in file Checking 'protein'.... WARNING: The unperturbed charge of the unit: -20.004200 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A and .R.A Warning: Close contact of 0.000084 angstroms between .R.A and .R.A Warning: Close contact of 0.000083 angstroms between .R.A and .R.A Warning: Close contact of 0.000088 angstroms between .R.A and .R.A Warning: Close contact of 0.000083 angstroms between .R.A and .R.A Warning: Close contact of 0.000008 angstroms between .R.A and .R.A Warning: Close contact of 0.000007 angstroms between .R.A and .R.A Warning: Close contact of 0.000110 angstroms between .R.A and .R.A Warning: Close contact of 0.000094 angstroms between .R.A and .R.A Warning: Close contact of 0.000041 angstroms between .R.A and .R.A Warning: Close contact of 0.000042 angstroms between .R.A and .R.A Warning: Close contact of 0.000017 angstroms between .R.A and .R.A Warning: Close contact of 0.000015 angstroms between .R.A and .R.A Warning: Close contact of 0.000075 angstroms between .R.A and .R.A Warning: Close contact of 0.000067 angstroms between .R.A and .R.A Warning: Close contact of 0.000013 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A
and .R.A Warning: Close contact of 0.000002 angstroms between .R.A
and .R.A Warning: Close contact of 0.000001 angstroms between .R.A

and .R.A Warning: Close contact of 1.209777 angstroms between .R.A and .R.A Warning: Close contact of 1.209915 angstroms between .R.A and .R.A Warning: Close contact of 1.209186 angstroms between .R.A and .R.A Warning: Close contact of 1.210581 angstroms between .R.A and .R.A Warning: Close contact of 1.210334 angstroms between .R.A and .R.A Warning: Close contact of 1.209886 angstroms between .R.A and .R.A Warning: Close contact of 1.210395 angstroms between .R.A and .R.A Warning: Close contact of 1.210054 angstroms between .R.A and .R.A Warning: Close contact of 1.209366 angstroms between .R.A and .R.A Warning: Close contact of 1.208981 angstroms between .R.A and .R.A Warning: Close contact of 1.208630 angstroms between .R.A and .R.A Warning: Close contact of 1.210853 angstroms between .R.A and .R.A Warning: Close contact of 1.210512 angstroms between .R.A and .R.A Warning: Close contact of 1.210277 angstroms between .R.A and .R.A Warning: Close contact of 1.210329 angstroms between .R.A and .R.A Warning: Close contact of 1.209641 angstroms between .R.A and .R.A Warning: Close contact of 1.211049 angstroms between .R.A and .R.A Warning: Close contact of 1.209882 angstroms between .R.A and .R.A Warning: Close contact of 1.210550 angstroms between .R.A and .R.A Warning: Close contact of 1.210403 angstroms between .R.A and .R.A Warning: Close contact of 1.211003 angstroms between .R.A and .R.A Warning: Close contact of 1.210648 angstroms between .R.A and .R.A Warning: Close contact of 1.209669 angstroms between .R.A and .R.A Warning: Close contact of 1.210904 angstroms between .R.A and .R.A Warning: Close contact of 1.210310 angstroms between .R.A and .R.A Warning: Close contact of 1.210393 angstroms between .R.A and .R.A Warning: Close contact of 1.209267 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000004 angstroms between .R.A and .R.A Warning: Close contact of 0.000004 angstroms between .R.A and .R.A Warning: Close contact of 0.000088 angstroms between .R.A and .R.A Warning: Close contact of 0.000107 angstroms between .R.A and .R.A Warning: Close contact of 0.000020 angstroms between .R.A and .R.A Warning: Close contact of 0.000021 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A and .R.A Warning: Close contact of 0.000012 angstroms between .R.A and .R.A Warning: Close contact of 0.000006 angstroms between .R.A and .R.A Warning: Close contact of 0.000102 angstroms between .R.A and .R.A Warning: Close contact of 0.000094 angstroms between .R.A and .R.A Warning: Close contact of 0.000011 angstroms between .R.A and .R.A Warning: Close contact of 0.000013 angstroms between .R.A and .R.A Warning: Close contact of 0.000014 angstroms between .R.A and .R.A Warning: Close contact of 0.000019 angstroms between .R.A and .R.A Warning: Close contact of 0.000004 angstroms between .R.A and .R.A Warning: Close contact of 0.000004 angstroms between .R.A and .R.A Warning: Close contact of 0.000021 angstroms between .R.A and .R.A Warning: Close contact of 0.000015 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A and .R.A Warning: Close contact of 0.000007 angstroms between .R.A
and .R.A Warning: Close contact of 0.000008 angstroms between .R.A
and .R.A Warning: Close contact of 0.000008 angstroms between .R.A

and .R.A Warning: Close contact of 1.209649 angstroms between .R.A and .R.A Warning: Close contact of 1.209378 angstroms between .R.A and .R.A Warning: Close contact of 1.210061 angstroms between .R.A and .R.A Warning: Close contact of 1.210158 angstroms between .R.A and .R.A Warning: Close contact of 1.210541 angstroms between .R.A and .R.A Warning: Close contact of 1.210536 angstroms between .R.A and .R.A Warning: Close contact of 1.209577 angstroms between .R.A and .R.A Warning: Close contact of 1.209501 angstroms between .R.A and .R.A Warning: Close contact of 1.210740 angstroms between .R.A and .R.A Warning: Close contact of 1.211133 angstroms between .R.A and .R.A Warning: Close contact of 1.210291 angstroms between .R.A and .R.A Warning: Close contact of 1.210198 angstroms between .R.A and .R.A Warning: Close contact of 1.210380 angstroms between .R.A and .R.A Warning: Close contact of 1.210461 angstroms between .R.A and .R.A Warning: Close contact of 1.210186 angstroms between .R.A and .R.A Warning: Close contact of 1.209446 angstroms between .R.A and .R.A Warning: Close contact of 1.210005 angstroms between .R.A and .R.A Warning: Close contact of 1.209909 angstroms between .R.A and .R.A Warning: Close contact of 1.209588 angstroms between .R.A and .R.A Warning: Close contact of 1.209186 angstroms between .R.A and .R.A Warning: Close contact of 1.210506 angstroms between .R.A and .R.A Warning: Close contact of 1.209074 angstroms between .R.A and .R.A Warning: Close contact of 1.209286 angstroms between .R.A and .R.A Warning: Close contact of 1.209998 angstroms between .R.A and .R.A Warning: Close contact of 1.208906 angstroms between .R.A and .R.A Warning: Close contact of 1.209411 angstroms between .R.A and .R.A Warning: Close contact of 1.210454 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000018 angstroms between .R.A and .R.A Warning: Close contact of 0.000020 angstroms between .R.A and .R.A Warning: Close contact of 0.000076 angstroms between .R.A and .R.A Warning: Close contact of 0.000079 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000072 angstroms between .R.A and .R.A Warning: Close contact of 0.000060 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000097 angstroms between .R.A and .R.A Warning: Close contact of 0.000103 angstroms between .R.A and .R.A Warning: Close contact of 0.000067 angstroms between .R.A and .R.A Warning: Close contact of 0.000054 angstroms between .R.A and .R.A Warning: Close contact of 0.000019 angstroms between .R.A and .R.A Warning: Close contact of 0.000020 angstroms between .R.A and .R.A Warning: Close contact of 0.000042 angstroms between .R.A and .R.A Warning: Close contact of 0.000052 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A
and .R.A Warning: Close contact of 0.000005 angstroms between .R.A
and .R.A Warning: Close contact of 0.000007 angstroms between .R.A

and .R.A Warning: Close contact of 1.210637 angstroms between .R.A and .R.A Warning: Close contact of 1.210259 angstroms between .R.A and .R.A Warning: Close contact of 1.209892 angstroms between .R.A and .R.A Warning: Close contact of 1.210747 angstroms between .R.A and .R.A Warning: Close contact of 1.209969 angstroms between .R.A and .R.A Warning: Close contact of 1.210701 angstroms between .R.A and .R.A Warning: Close contact of 1.210419 angstroms between .R.A and .R.A Warning: Close contact of 1.210282 angstroms between .R.A and .R.A Warning: Close contact of 1.208976 angstroms between .R.A and .R.A Warning: Close contact of 1.209656 angstroms between .R.A and .R.A Warning: Close contact of 1.210361 angstroms between .R.A and .R.A Warning: Close contact of 1.209953 angstroms between .R.A and .R.A Warning: Close contact of 1.210712 angstroms between .R.A and .R.A Warning: Close contact of 1.209978 angstroms between .R.A and .R.A Warning: Close contact of 1.208846 angstroms between .R.A and .R.A Warning: Close contact of 1.209396 angstroms between .R.A and .R.A Warning: Close contact of 1.208889 angstroms between .R.A and .R.A Warning: Close contact of 1.210180 angstroms between .R.A and .R.A Warning: Close contact of 1.209817 angstroms between .R.A and .R.A Warning: Close contact of 1.209385 angstroms between .R.A and .R.A Warning: Close contact of 1.209953 angstroms between .R.A and .R.A Warning: Close contact of 1.209437 angstroms between .R.A and .R.A Warning: Close contact of 1.210641 angstroms between .R.A and .R.A Warning: Close contact of 1.209204 angstroms between .R.A and .R.A Warning: Close contact of 1.209217 angstroms between .R.A and .R.A Warning: Close contact of 1.210347 angstroms between .R.A and .R.A Warning: Close contact of 1.209090 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000011 angstroms between .R.A and .R.A Warning: Close contact of 0.000009 angstroms between .R.A and .R.A Warning: Close contact of 0.000011 angstroms between .R.A and .R.A Warning: Close contact of 0.000018 angstroms between .R.A and .R.A Warning: Close contact of 0.000024 angstroms between .R.A and .R.A Warning: Close contact of 0.000027 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A and .R.A Warning: Close contact of 0.000003 angstroms between .R.A and .R.A Warning: Close contact of 0.000057 angstroms between .R.A and .R.A Warning: Close contact of 0.000048 angstroms between .R.A and .R.A Warning: Close contact of 0.000030 angstroms between .R.A and .R.A Warning: Close contact of 0.000026 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000008 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A
and .R.A Warning: Close contact of 0.000005 angstroms between .R.A
and .R.A Warning: Close contact of 0.000003 angstroms between .R.A

and .R.A Warning: Close contact of 1.210165 angstroms between .R.A and .R.A Warning: Close contact of 1.209836 angstroms between .R.A and .R.A Warning: Close contact of 1.211024 angstroms between .R.A and .R.A Warning: Close contact of 1.209686 angstroms between .R.A and .R.A Warning: Close contact of 1.209726 angstroms between .R.A and .R.A Warning: Close contact of 1.209164 angstroms between .R.A and .R.A Warning: Close contact of 1.209876 angstroms between .R.A and .R.A Warning: Close contact of 1.210029 angstroms between .R.A and .R.A Warning: Close contact of 1.210030 angstroms between .R.A and .R.A Warning: Close contact of 1.209702 angstroms between .R.A and .R.A Warning: Close contact of 1.210531 angstroms between .R.A and .R.A Warning: Close contact of 1.210130 angstroms between .R.A and .R.A Warning: Close contact of 1.209830 angstroms between .R.A and .R.A Warning: Close contact of 1.210234 angstroms between .R.A and .R.A Warning: Close contact of 1.210379 angstroms between .R.A and .R.A Warning: Close contact of 1.209605 angstroms between .R.A and .R.A Warning: Close contact of 1.208937 angstroms between .R.A and .R.A Warning: Close contact of 1.210194 angstroms between .R.A and .R.A Warning: Close contact of 1.209930 angstroms between .R.A and .R.A Warning: Close contact of 1.210634 angstroms between .R.A and .R.A Warning: Close contact of 1.209656 angstroms between .R.A and .R.A Warning: Close contact of 1.208756 angstroms between .R.A and .R.A Warning: Close contact of 1.210121 angstroms between .R.A and .R.A Warning: Close contact of 1.210011 angstroms between .R.A and .R.A Warning: Close contact of 1.209414 angstroms between .R.A and .R.A Warning: Close contact of 1.210221 angstroms between .R.A and .R.A Warning: Close contact of 1.210778 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000016 angstroms between .R.A and .R.A Warning: Close contact of 0.000018 angstroms between .R.A and .R.A Warning: Close contact of 0.000074 angstroms between .R.A and .R.A Warning: Close contact of 0.000073 angstroms between .R.A and .R.A Warning: Close contact of 0.000028 angstroms between .R.A and .R.A Warning: Close contact of 0.000026 angstroms between .R.A and .R.A Warning: Close contact of 0.000035 angstroms between .R.A and .R.A Warning: Close contact of 0.000039 angstroms between .R.A and .R.A Warning: Close contact of 0.000001 angstroms between .R.A and .R.A Warning: Close contact of 0.000002 angstroms between .R.A and .R.A Warning: Close contact of 0.000027 angstroms between .R.A and .R.A Warning: Close contact of 0.000036 angstroms between .R.A and .R.A Warning: Close contact of 0.000048 angstroms between .R.A and .R.A Warning: Close contact of 0.000054 angstroms between .R.A and .R.A Warning: Close contact of 0.000003 angstroms between .R.A and .R.A Warning: Close contact of 0.000008 angstroms between .R.A and .R.A Warning: Close contact of 0.000020 angstroms between .R.A and .R.A Warning: Close contact of 0.000023 angstroms between .R.A and .R.A Warning: Close contact of 0.000006 angstroms between .R.A and .R.A Warning: Close contact of 0.000006 angstroms between .R.A and .R.A Warning: Close contact of 0.000005 angstroms between .R.A and .R.A Warning: Close contact of 0.000006 angstroms between .R.A
and .R.A Warning: Close contact of 0.000024 angstroms between .R.A
and .R.A Warning: Close contact of 0.000015 angstroms between .R.A

and .R.A Warning: Close contact of 1.210889 angstroms between .R.A and .R.A Warning: Close contact of 1.211181 angstroms between .R.A and .R.A Warning: Close contact of 1.209604 angstroms between .R.A and .R.A Warning: Close contact of 1.209401 angstroms between .R.A and .R.A Warning: Close contact of 1.210530 angstroms between .R.A and .R.A Warning: Close contact of 1.210420 angstroms between .R.A and .R.A Warning: Close contact of 1.209115 angstroms between .R.A and .R.A Warning: Close contact of 1.211146 angstroms between .R.A and .R.A Warning: Close contact of 1.209171 angstroms between .R.A and .R.A Warning: Close contact of 1.210709 angstroms between .R.A and .R.A Warning: Close contact of 1.210406 angstroms between .R.A and .R.A Warning: Close contact of 1.209422 angstroms between .R.A and .R.A Warning: Close contact of 1.210114 angstroms between .R.A and .R.A Warning: Close contact of 1.209451 angstroms between .R.A and .R.A Warning: Close contact of 1.209270 angstroms between .R.A and .R.A Warning: Close contact of 1.209947 angstroms between .R.A and .R.A Warning: Close contact of 1.210178 angstroms between .R.A and .R.A Warning: Close contact of 1.209794 angstroms between .R.A and .R.A Warning: Close contact of 1.210793 angstroms between .R.A and .R.A Warning: Close contact of 1.208661 angstroms between .R.A and .R.A Warning: Close contact of 1.210621 angstroms between .R.A and .R.A Warning: Close contact of 1.209936 angstroms between .R.A and .R.A Warning: Close contact of 1.209773 angstroms between .R.A and .R.A Warning: Close contact of 1.210781 angstroms between .R.A and .R.A Warning: Close contact of 1.211300 angstroms between .R.A and .R.A Warning: Close contact of 1.209176 angstroms between .R.A and .R.A Warning: Close contact of 1.210070 angstroms between .R.A and .R.A Checking parameters for unit 'protein'. Checking for bond parameters. Checking for angle parameters. check: Errors: 135 Warnings: 271 20 Na+ ions required to neutralize. Adding 20 counter ions to "protein" using 1A grid Used default radius 1.50 for 135 atoms Grid extends from solute vdw + 5.15 to 11.15 Resolution: 1.00 Angstrom. grid build: 1 sec (no solvent present) Calculating grid charges charges: 32 sec Placed Na+ in protein at (48.12, -2.01, 6.84). Placed Na+ in protein at (54.12, 8.99, 5.84). Placed Na+ in protein at (37.12, -12.01, 25.84). Placed Na+ in protein at (29.12, 28.99, -11.16). Placed Na+ in protein at (26.12, 19.99, -15.16). Placed Na+ in protein at (28.12, 28.99, 18.84). Placed Na+ in protein at (11.12, 0.99, 56.84). Placed Na+ in protein at (42.12, 20.99, -9.16). Placed Na+ in protein at (67.12, -1.01, 24.84). Placed Na+ in protein at (40.12, -6.01, 6.84). Placed Na+ in protein at (-7.88, 10.99, 63.84). Placed Na+ in protein at (75.12, 13.99, 24.84). Placed Na+ in protein at (11.12, 26.99, 0.84). Placed Na+ in protein at (24.12, 20.99, 54.84). Placed Na+ in protein at (1.12, 5.99, -28.16). Placed Na+ in protein at (-7.88, -5.01, 11.84). Placed Na+ in protein at (48.12, -5.01, 44.84). Placed Na+ in protein at (48.12, 27.99, 48.84). Placed Na+ in protein at (45.12, 31.99, -3.16). Placed Na+ in protein at (30.12, -2.01, -21.16). Done adding ions. Scaling up box by a factor of 1.292063 to meet diagonal cut criterion Solute vdw bounding box: 95.149 55.155 92.519 Total bounding box for atom centers: 120.990 120.990 120.990 (box expansion for 'iso' is 52.7%) Solvent unit box: 18.774 18.774 18.774 Volume: 907695.449 A^3 (oct) Mass > 494154.440 amu, Density > 0.904 g/cc (type - hence mass - of one or more atoms could not be found) Added 23654 residues. Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. Quit [senthil@craycx1 test3]$