>> logFile leap.log log started: Mon Dec 9 17:38:26 2013 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /hpctmp/a0068362/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.5, January 2013) > > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /hpctmp/a0068362/amber12/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > UNK = loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named UNK > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > saveoff UNK ligand.lib Saving UNK. Building topology. Building atom parameters. > saveamberparm UNK ligand.prmtop ligand.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 23 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected UNK 1 ) (no restraints) > receptor = loadpdb 4HW4.pdb Loading PDB file: ./4HW4.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY. (Residue 1: ASP, Nonterminal, was not found in name map.) (Residue 2: GLU, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: TYR, Nonterminal, was not found in name map.) (Residue 5: ARG, Nonterminal, was not found in name map.) (Residue 6: GLN, Nonterminal, was not found in name map.) (Residue 7: SER, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLU, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: ILE, Nonterminal, was not found in name map.) (Residue 12: SER, Nonterminal, was not found in name map.) (Residue 13: ARG, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: GLU, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ALA, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: ALA, Nonterminal, was not found in name map.) (Residue 23: LYS, Nonterminal, was not found in name map.) (Residue 24: ASP, Nonterminal, was not found in name map.) (Residue 25: THR, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: PRO, Nonterminal, was not found in name map.) (Residue 28: MET, Nonterminal, was not found in name map.) (Residue 29: GLY, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: SER, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ALA, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: SER, Nonterminal, was not found in name map.) (Residue 36: ARG, Nonterminal, was not found in name map.) (Residue 37: LYS, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: GLU, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: ARG, Nonterminal, was not found in name map.) (Residue 44: ARG, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: ASP, Nonterminal, was not found in name map.) (Residue 48: GLY, Nonterminal, was not found in name map.) (Residue 49: VAL, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: ARG, Nonterminal, was not found in name map.) (Residue 52: ASN, Nonterminal, was not found in name map.) (Residue 53: HIS, Nonterminal, was not found in name map.) (Residue 54: GLU, Nonterminal, was not found in name map.) (Residue 55: THR, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: PHE, Nonterminal, was not found in name map.) (Residue 58: GLN, Nonterminal, was not found in name map.) (Residue 59: GLY, Nonterminal, was not found in name map.) (Residue 60: MET, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: ARG, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: ASP, Nonterminal, was not found in name map.) (Residue 66: ILE, Nonterminal, was not found in name map.) (Residue 67: LYS, Nonterminal, was not found in name map.) (Residue 68: ASN, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: ASP, Nonterminal, was not found in name map.) (Residue 71: ASP, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: LYS, Nonterminal, was not found in name map.) (Residue 74: SER, Nonterminal, was not found in name map.) (Residue 75: LEU, Nonterminal, was not found in name map.) (Residue 76: SER, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: VAL, Nonterminal, was not found in name map.) (Residue 79: MET, Nonterminal, was not found in name map.) (Residue 80: ILE, Nonterminal, was not found in name map.) (Residue 81: HIS, Nonterminal, was not found in name map.) (Residue 82: VAL, Nonterminal, was not found in name map.) (Residue 83: PHE, Nonterminal, was not found in name map.) (Residue 84: SER, Nonterminal, was not found in name map.) (Residue 85: ASP, Nonterminal, was not found in name map.) (Residue 86: GLY, Nonterminal, was not found in name map.) (Residue 87: VAL, Nonterminal, was not found in name map.) (Residue 88: THR, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: TRP, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: ARG, Nonterminal, was not found in name map.) (Residue 93: ILE, Nonterminal, was not found in name map.) (Residue 94: VAL, Nonterminal, was not found in name map.) (Residue 95: THR, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ILE, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: GLY, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: PHE, Nonterminal, was not found in name map.) (Residue 103: VAL, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: LYS, Nonterminal, was not found in name map.) (Residue 106: HIS, Nonterminal, was not found in name map.) (Residue 107: LEU, Nonterminal, was not found in name map.) (Residue 108: LYS, Nonterminal, was not found in name map.) (Residue 109: THR, Nonterminal, was not found in name map.) (Residue 110: ILE, Nonterminal, was not found in name map.) (Residue 111: ASN, Nonterminal, was not found in name map.) (Residue 112: GLN, Nonterminal, was not found in name map.) (Residue 113: GLU, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: CYS, Nonterminal, was not found in name map.) (Residue 116: ILE, Nonterminal, was not found in name map.) (Residue 117: GLU, Nonterminal, was not found in name map.) (Residue 118: PRO, Nonterminal, was not found in name map.) (Residue 119: LEU, Nonterminal, was not found in name map.) (Residue 120: ALA, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: SER, Nonterminal, was not found in name map.) (Residue 123: ILE, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: ASP, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: LEU, Nonterminal, was not found in name map.) (Residue 128: VAL, Nonterminal, was not found in name map.) (Residue 129: ARG, Nonterminal, was not found in name map.) (Residue 130: THR, Nonterminal, was not found in name map.) (Residue 131: LYS, Nonterminal, was not found in name map.) (Residue 132: ARG, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: TRP, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: VAL, Nonterminal, was not found in name map.) (Residue 137: LYS, Nonterminal, was not found in name map.) (Residue 138: GLN, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: GLY, Nonterminal, was not found in name map.) (Residue 141: TRP, Nonterminal, was not found in name map.) (Residue 142: ASP, Nonterminal, was not found in name map.) (Residue 143: GLY, Nonterminal, was not found in name map.) (Residue 144: PHE, Nonterminal, was not found in name map.) (Residue 145: VAL, Nonterminal, was not found in name map.) (Residue 146: GLU, Nonterminal, was not found in name map.) (Residue 147: PHE, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: HIS, Nonterminal, was not found in name map.) (Residue 150: VAL, Nonterminal, was not found in name map.) (Residue 151: GLU, Nonterminal, was not found in name map.) (Residue 152: ASP, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 153 to: CLEU. Joining NGLY - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - TYR Joining TYR - ARG Joining ARG - GLN Joining GLN - SER Joining SER - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - ILE Joining ILE - SER Joining SER - ARG Joining ARG - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ALA Joining ALA - THR Joining THR - GLY Joining GLY - ALA Joining ALA - LYS Joining LYS - ASP Joining ASP - THR Joining THR - LYS Joining LYS - PRO Joining PRO - MET Joining MET - GLY Joining GLY - ARG Joining ARG - SER Joining SER - GLY Joining GLY - ALA Joining ALA - THR Joining THR - SER Joining SER - ARG Joining ARG - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ASN Joining ASN - HIE Joining HIE - GLU Joining GLU - THR Joining THR - ALA Joining ALA - PHE Joining PHE - GLN Joining GLN - GLY Joining GLY - MET Joining MET - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - LEU Joining LEU - ASP Joining ASP - ILE Joining ILE - LYS Joining LYS - ASN Joining ASN - GLU Joining GLU - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - SER Joining SER - LEU Joining LEU - SER Joining SER - ARG Joining ARG - VAL Joining VAL - MET Joining MET - ILE Joining ILE - HIE Joining HIE - VAL Joining VAL - PHE Joining PHE - SER Joining SER - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - THR Joining THR - ASN Joining ASN - TRP Joining TRP - GLY Joining GLY - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - THR Joining THR - LEU Joining LEU - ILE Joining ILE - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - PHE Joining PHE - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - HIE Joining HIE - LEU Joining LEU - LYS Joining LYS - THR Joining THR - ILE Joining ILE - ASN Joining ASN - GLN Joining GLN - GLU Joining GLU - SER Joining SER - CYS Joining CYS - ILE Joining ILE - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - SER Joining SER - ILE Joining ILE - THR Joining THR - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - THR Joining THR - LYS Joining LYS - ARG Joining ARG - ASP Joining ASP - TRP Joining TRP - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLN Joining GLN - ARG Joining ARG - GLY Joining GLY - TRP Joining TRP - ASP Joining ASP - GLY Joining GLY - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - PHE Joining PHE - PHE Joining PHE - HIE Joining HIE - VAL Joining VAL - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ASP - CLEU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1227 Leap added 1258 missing atoms according to residue templates: 11 Heavy 1247 H / lone pairs > saveamberparm receptor receptor.prmtop receptor.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 2.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 496 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CLEU 1 NGLY 1 ) (no restraints) > savepdb receptor receptor.pdb Writing pdb file: receptor.pdb Converting N-terminal residue name to PDB format: NGLY -> GLY Converting C-terminal residue name to PDB format: CLEU -> LEU > saveoff receptor receptor.lib Saving receptor. Building topology. Building atom parameters. > comp = combine {receptor UNK} Sequence: default_name Sequence: UNK > saveamberparm comp complex.prmtop complex.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.999800 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for 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 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 total 519 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CLEU 1 NGLY 1 UNK 1 ) (no restraints) > savepdb comp complex.pdb Writing pdb file: complex.pdb Converting N-terminal residue name to PDB format: NGLY -> GLY Converting C-terminal residue name to PDB format: CLEU -> LEU > saveoff comp complex.lib Saving comp. Building topology. Building atom parameters. > charge comp Total unperturbed charge: 1.999800 Total perturbed charge: 1.999800 > addions comp CL- 2 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. > charge comp Total unperturbed charge: 1.999800 Total perturbed charge: 1.999800 > addions comp Cl- 2 Adding 2 counter ions to "comp" using 1A grid Total solute charge: 2.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.51 to 8.51 Box: enclosing: -38.65 -41.55 -32.01 18.01 26.32 30.36 sized: 89.35 86.45 95.99 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 0 sec Volume = 2.16% of box, grid points 45318 (no solvent present) Calculating grid charges charges: 2 sec Placed Cl- in comp at (1.35, -19.55, -2.01). Placed Cl- in comp at (-31.65, 7.45, -11.01). Done adding ions. > charge comp Total unperturbed charge: -0.000200 Total perturbed charge: -0.000200 > savepdb comp complex_ionated.pdb Writing pdb file: complex_ionated.pdb Converting N-terminal residue name to PDB format: NGLY -> GLY Converting C-terminal residue name to PDB format: CLEU -> LEU > solvateoct comp TIP3PBOX 12.0 Scaling up box by a factor of 1.284245 to meet diagonal cut criterion Solute vdw bounding box: 46.902 45.724 49.683 Total bounding box for atom centers: 80.504 80.504 80.504 (box expansion for 'iso' is 8.9%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 270716.084 A^3 (oct) Total mass 144252.706 amu, Density 0.885 g/cc Added 6999 residues. > saveamberparm comp complex_solvated.prmtop complex_solvated.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for 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 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 total 519 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CLEU 1 NGLY 1 UNK 1 WAT 6999 ) (no restraints) > savepdb comp complex_solvated.pdb Writing pdb file: complex_solvated.pdb Converting N-terminal residue name to PDB format: NGLY -> GLY Converting C-terminal residue name to PDB format: CLEU -> LEU > saveoff comp complex_solvated.lib Creating complex_solvated.lib Saving comp. Building topology. Building atom parameters. > quit Quit