-I: Adding /soft/amber8/dat/leap/prep to search path. -I: Adding /soft/amber8/dat/leap/lib to search path. -I: Adding /soft/amber8/dat/leap/parm to search path. -I: Adding /soft/amber8/dat/leap/cmd to search path. -f: Source teleap.in. Welcome to LEaP! Sourcing leaprc: ./leaprc ----- Source: /soft/amber8/dat/leap/cmd/leaprc.gaff ----- Source of /soft/amber8/dat/leap/cmd/leaprc.gaff done Log ./leap.log Loading parameters: /soft/amber8/dat/leap/parm/gaff.dat ----- Source: /soft/amber8/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber8/dat/leap/cmd/leaprc.ff03 done Log ./leap.log Loading parameters: /soft/amber8/dat/leap/parm/parm99.dat Loading parameters: /soft/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) Loading library: /soft/amber8/dat/leap/lib/all_amino03.lib Loading library: ./ions94.lib Loading library: /soft/amber8/dat/leap/lib/solvents.lib Loading library: /soft/amber8/dat/leap/lib/all_nucleic94.lib Loading library: /soft/amber8/dat/leap/lib/all_aminoct94.lib Loading library: /soft/amber8/dat/leap/lib/all_aminont94.lib ----- Source: /soft/amber8/dat/leap/cmd/leaprc.rna.ff98 ----- Source of /soft/amber8/dat/leap/cmd/leaprc.rna.ff98 done Log ./leap.log Loading parameters: /soft/amber8/dat/leap/parm/parm98.dat Loading library: /soft/amber8/dat/leap/lib/all_nucleic94.lib Loading library: /soft/amber8/dat/leap/lib/all_amino94.lib Loading library: /soft/amber8/dat/leap/lib/all_aminoct94.lib Loading library: /soft/amber8/dat/leap/lib/all_aminont94.lib Loading library: ./ions94.lib Loading library: /soft/amber8/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 -> RG5 for 0GUA -> DG5 Substituting map 1GUA -> RG3 for 1GUA -> DG3 Substituting map GUA -> RG for GUA -> DG Substituting map 0ADE -> RA5 for 0ADE -> DA5 Substituting map 1ADE -> RA3 for 1ADE -> DA3 Substituting map ADE -> RA for ADE -> DA Substituting map 0CYT -> RC5 for 0CYT -> DC5 Substituting map 1CYT -> RC3 for 1CYT -> DC3 Substituting map CYT -> RC for CYT -> DC Substituting map 0G -> RG5 for 0G -> DG5 Substituting map 1G -> RG3 for 1G -> DG3 Substituting map G -> RG for G -> DG Substituting map GN -> RGN for GN -> DGN Substituting map 0A -> RA5 for 0A -> DA5 Substituting map 1A -> RA3 for 1A -> DA3 Substituting map A -> RA for A -> DA Substituting map AN -> RAN for AN -> DAN Substituting map 0C -> RC5 for 0C -> DC5 Substituting map 1C -> RC3 for 1C -> DC3 Substituting map C -> RC for C -> DC Substituting map CN -> RCN for CN -> DCN Substituting map 0C5 -> RC5 for 0C5 -> DC5 Substituting map 0G5 -> RG5 for 0G5 -> DG5 Substituting map 0A5 -> RA5 for 0A5 -> DA5 Substituting map 1C3 -> RC3 for 1C3 -> DC3 Substituting map 1G3 -> RG3 for 1G3 -> DG3 Substituting map 1A3 -> RA3 for 1A3 -> DA3 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 O1' -> O4' for O1' -> O4' Substituting map OA -> O1P for OA -> O1P Substituting map OB -> O2P for OB -> O2P Substituting map H5*1 -> H5'1 for H5*1 -> H5'1 Substituting map H5*2 -> H5'2 for H5*2 -> H5'2 Substituting map H4* -> H4' for H4* -> H4' Substituting map H3* -> H3' for H3* -> H3' Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2'1 for H2*1 -> H2'1 Sourcing: ./teleap.in Loading parameters: ./TSB.frcmod Reading force field mod type file (frcmod) Loading parameters: ./AET.frcmod Reading force field mod type file (frcmod) Loading parameters: ./5MU.frcmod Reading force field mod type file (frcmod) Unknown keyword: in parameter file. Unknown keyword: in parameter file. Loading parameters: ./DHU.frcmod Reading force field mod type file (frcmod) Unknown keyword: in parameter file. Unknown keyword: in parameter file. Loading parameters: ./PSU.frcmod Reading force field mod type file (frcmod) Unknown keyword: in parameter file. Unknown keyword: in parameter file. Loading parameters: ./7MG.frcmod Reading force field mod type file (frcmod) Unknown keyword: in parameter file. Unknown keyword: in parameter file. Loading Prep ./TSB.in Loading Prep ./AET.in Loading Prep ./5MU.prepin Loading Prep ./DHU.prepin Loading Prep ./PSU.prepin Loading Prep ./7MG.prepin Loading PDB ./prot.pdb -- residue 1436: duplicate [ C1] atoms (total 2) -- residue 1436: duplicate [ C10] atoms (total 2) -- residue 1436: duplicate [ C11] atoms (total 2) -- residue 1436: duplicate [ C12] atoms (total 2) -- residue 1436: duplicate [ C13] atoms (total 2) -- residue 1436: duplicate [ C14] atoms (total 2) -- residue 1436: duplicate [ C2] atoms (total 2) -- residue 1436: duplicate [ C3] atoms (total 2) -- residue 1436: duplicate [ C4] atoms (total 2) -- residue 1436: duplicate [ C5] atoms (total 2) -- residue 1436: duplicate [ C6] atoms (total 2) -- residue 1436: duplicate [ C7] atoms (total 2) -- residue 1436: duplicate [ C8] atoms (total 2) -- residue 1436: duplicate [ C9] atoms (total 2) -- residue 1436: duplicate [ N1] atoms (total 2) -- residue 1436: duplicate [ N2] atoms (total 2) -- residue 1436: duplicate [ N3] atoms (total 2) -- residue 1436: duplicate [ N4] atoms (total 2) -- residue 1436: duplicate [ N5] atoms (total 2) -- residue 1436: duplicate [ N6] atoms (total 2) -- residue 1436: duplicate [ O1] atoms (total 2) -- residue 1436: duplicate [ O2] atoms (total 2) -- residue 1436: duplicate [ O3] atoms (total 2) -- residue 1436: duplicate [ O4] atoms (total 2) -- residue 1436: duplicate [ O5] atoms (total 2) -- residue 1436: duplicate [ O6] atoms (total 2) -- residue 1436: duplicate [ O7] atoms (total 2) -- residue 1436: duplicate [ O8] atoms (total 2) -- residue 1436: duplicate [ O9] atoms (total 2) -- residue 1436: duplicate [ P1] atoms (total 2) -- residue 1437: duplicate [Zn] atoms (total 2) ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE: (same-name atoms are reduced to a single atom) Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in 13704 Leap added 11856 missing atoms according to residue templates: 2 Heavy 11854 H / lone pairs addIons: Argument #2 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. Solute vdw bounding box: 114.054 109.400 163.502 Total bounding box for atom centers: 134.054 129.400 183.502 Solvent unit box: 18.774 18.774 18.774 Total vdw box size: 137.380 132.884 186.394 angstroms. Volume: 3402734.397 A^3 Total mass 1853019.646 amu, Density 0.904 g/cc Added 91899 residues. Checking Unit. WARNING: There is a bond of 0.162076 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 14.458799 angstroms between: ------- .R.A and .R.A

WARNING: There is a bond of 0.161591 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 14.458661 angstroms between: ------- .R.A and .R.A

WARNING: The unperturbed charge of the unit: -181.000120 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Could not find bond parameter for: OS - oh Could not find bond parameter for: o - P Could not find bond parameter for: OS - oh Could not find bond parameter for: o - P Building angle parameters. Could not find angle parameter: OS - oh - ho Could not find angle parameter: OS - oh - p5 Could not find angle parameter: CT - OS - oh Could not find angle parameter: o - P - O2 Could not find angle parameter: o - P - O2 Could not find angle parameter: o - P - OS Could not find angle parameter: c - o - P Could not find angle parameter: OS - oh - ho Could not find angle parameter: OS - oh - p5 Could not find angle parameter: CT - OS - oh Could not find angle parameter: o - P - O2 Could not find angle parameter: o - P - O2 Could not find angle parameter: o - P - OS Could not find angle parameter: c - o - P Building proper torsion parameters. ** No torsion terms for CT-OS-oh-ho ** No torsion terms for CT-OS-oh-p5 ** No torsion terms for oh-c-o-P ** No torsion terms for c-o-P-O2 ** No torsion terms for c-o-P-O2 ** No torsion terms for c-o-P-OS ** No torsion terms for c3-c-o-P ** No torsion terms for CT-OS-oh-ho ** No torsion terms for CT-OS-oh-p5 ** No torsion terms for oh-c-o-P ** No torsion terms for c-o-P-O2 ** No torsion terms for c-o-P-O2 ** No torsion terms for c-o-P-OS ** No torsion terms for c3-c-o-P Building improper torsion parameters. old PREP-specified impropers: : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C6 C1 N1 C2 : H2 N1 C2 N2 : C3 N1 C1 N3 : H1 N3 C4 N4 : C1 C5 C3 N2 : C3 N5 C5 N4 : C11 C12 N5 C5 : N5 N6 C12 O8 : C13 O9 C14 O10 <7MG 1329>: C4 C8 N9 C1' <7MG 1329>: H8 N7 C8 N9 <7MG 1329>: C5 C8 N7 C10 <7MG 1329>: C6 C4 C5 N7 <7MG 1329>: C5 N1 C6 O6 <7MG 1329>: N2 N1 C2 N3 <7MG 1329>: C5 N9 C4 N3 <5MU 1337>: N1 N3 C2 O2 <5MU 1337>: C5 N3 C4 O4 <5MU 1337>: C4 C6 C5 C10 <5MU 1337>: C5 H6 C6 N1 : C4 C6 C5 C1' : C5 N3 C4 O4 : N3 N1 C2 O2 : C5 H6 C6 N1 : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C2 C1' N1 C6 : N1 N3 C2 O2 : C2 C4 N3 H3 : C5 N3 C4 O4 : C6 C1 N1 C2 : H2 N1 C2 N2 : C3 N1 C1 N3 : H1 N3 C4 N4 : C1 C5 C3 N2 : C3 N5 C5 N4 : C11 C12 N5 C5 : N5 N6 C12 O8 : C13 O9 C14 O10 <7MG 1405>: C4 C8 N9 C1' <7MG 1405>: H8 N7 C8 N9 <7MG 1405>: C5 C8 N7 C10 <7MG 1405>: C6 C4 C5 N7 <7MG 1405>: C5 N1 C6 O6 <7MG 1405>: N2 N1 C2 N3 <7MG 1405>: C5 N9 C4 N3 <5MU 1413>: N1 N3 C2 O2 <5MU 1413>: C5 N3 C4 O4 <5MU 1413>: C4 C6 C5 C10 <5MU 1413>: C5 H6 C6 N1 : C4 C6 C5 C1' : C5 N3 C4 O4 : N3 N1 C2 O2 : C5 H6 C6 N1 : C12 O8 C11 O3 : C6 C1 N1 C2 : H4 N1 C2 N2 : C3 N1 C1 N3 : C1 C5 C3 N2 : C3 N4 C5 N5 : C5 H1 N5 H2 : H3 N4 C4 N3 total 5091 improper torsions applied 80 improper torsions in old prep form Building H-Bond parameters. Parameter file was not saved. Quit