> HPüRclptMACSleap.logûäúän>¥>> # >> # ----- 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" } >> { "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" } >> { "pd" "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: /usr/local/amber8/dat/leap/parm/gaff.dat > > pore = loadpdb "pore_deprotonated.pdb" Loading PDB file: ./pore_deprotonated.pdb 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: THR, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: TRP, Nonterminal, was not found in name map.) (Residue 6: ALA, Nonterminal, was not found in name map.) (Residue 7: PHE, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: PHE, Nonterminal, was not found in name map.) (Residue 12: ARG, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: THR, Nonterminal, was not found in name map.) (Residue 16: GLN, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: TYR, Nonterminal, was not found in name map.) (Residue 19: TRP, Nonterminal, was not found in name map.) (Residue 20: GLU, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: SER, Nonterminal, was not found in name map.) (Residue 24: PRO, Nonterminal, was not found in name map.) (Residue 25: SER, Nonterminal, was not found in name map.) (Residue 26: THR, Nonterminal, was not found in name map.) (Residue 27: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 28 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 29 to: NGLY. (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: PHE, Nonterminal, was not found in name map.) (Residue 34: HIS, Nonterminal, was not found in name map.) (Residue 35: SER, Nonterminal, was not found in name map.) (Residue 36: PHE, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: VAL, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: ILE, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: CYS, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: GLU, Nonterminal, was not found in name map.) (Residue 47: TRP, Nonterminal, was not found in name map.) (Residue 48: ILE, Nonterminal, was not found in name map.) (Residue 49: GLU, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: TYR, Nonterminal, was not found in name map.) (Residue 52: SER, Nonterminal, was not found in name map.) (Residue 53: PRO, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: THR, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 57 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 58 to: NGLY. (Residue 59: ASP, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: GLY, Nonterminal, was not found in name map.) (Residue 63: LEU, Nonterminal, was not found in name map.) (Residue 64: GLY, Nonterminal, was not found in name map.) (Residue 65: TYR, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: SER, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LEU, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: LYS, Nonterminal, was not found in name map.) (Residue 76: GLY, Nonterminal, was not found in name map.) (Residue 77: TRP, Nonterminal, was not found in name map.) (Residue 78: MET, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: TYR, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: SER, Nonterminal, was not found in name map.) (Residue 84: THR, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 86 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 87 to: NGLY. (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: PHE, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: SER, Nonterminal, was not found in name map.) (Residue 94: ILE, Nonterminal, was not found in name map.) (Residue 95: ILE, Nonterminal, was not found in name map.) (Residue 96: CYS, Nonterminal, was not found in name map.) (Residue 97: LEU, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: GLU, Nonterminal, was not found in name map.) (Residue 100: ILE, Nonterminal, was not found in name map.) (Residue 101: THR, Nonterminal, was not found in name map.) (Residue 102: THR, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: GLY, Nonterminal, was not found in name map.) (Residue 106: TRP, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: TYR, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: SER, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 115 to: CLEU. Joining NGLY - ASP Joining ASP - THR Joining THR - PHE Joining PHE - SER Joining SER - TRP Joining TRP - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ARG Joining ARG - LEU Joining LEU - MET Joining MET - THR Joining THR - GLN Joining GLN - ASP Joining ASP - TYR Joining TYR - TRP Joining TRP - GLU Joining GLU - ASN Joining ASN - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - ASN Joining ASN - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - HIE Joining HIE - SER Joining SER - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - TRP Joining TRP - ILE Joining ILE - GLU Joining GLU - THR Joining THR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - ASP Joining ASP - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - THR Joining THR - PHE Joining PHE - LYS Joining LYS - GLY Joining GLY - TRP Joining TRP - MET Joining MET - ASP Joining ASP - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - GLU Joining GLU - THR Joining THR - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - CYS Joining CYS - LEU Joining LEU - PHE Joining PHE - GLU Joining GLU - ILE Joining ILE - THR Joining THR - THR Joining THR - SER Joining SER - ALA Joining ALA - GLY Joining GLY - TRP Joining TRP - ASP Joining ASP - GLY Joining GLY - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 906 Leap added 886 missing atoms according to residue templates: 18 Heavy 868 H / lone pairs > stx = loadmol2 stxagain.mol2 Loading Mol2 file: ./stxagain.mol2 > complex = createunit complex > complex = combine { pore stx } Sequence: Sequence: stx > savepdb complex "c3.pdb" Writing pdb file: c3.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > savepdb stx "stxmin.pdb" Writing pdb file: stxmin.pdb > savepdb pore "pore.pdb" Writing pdb file: pore.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > saveamberparm stx stx.prmtop stx.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.999900 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 c3-c2-nh-hn atoms are: C C7 N5 H5 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N5 N3 C7 N4 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C1 C7 N3 H3 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C2 C3 N HN ** Warning: No sp2 improper torsion term for c3-c3-nh-c2 atoms are: C1 C4 N2 C3 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N N2 C3 N1 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C3 H11 N1 H12 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C7 H41 N4 H42 total 2 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected stx 1 ) (no restraints) > saveamberparm pore pore.prmtop pore.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -8.000000 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 ** 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 394 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. }J>> # >> # ----- 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" } >> { "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" } >> { "pd" "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: /usr/local/amber8/dat/leap/parm/gaff.dat > > pore = loadpdb "pore_deprotonated.pdb" Loading PDB file: ./pore_deprotonated.pdb 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: THR, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: TRP, Nonterminal, was not found in name map.) (Residue 6: ALA, Nonterminal, was not found in name map.) (Residue 7: PHE, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: PHE, Nonterminal, was not found in name map.) (Residue 12: ARG, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: THR, Nonterminal, was not found in name map.) (Residue 16: GLN, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: TYR, Nonterminal, was not found in name map.) (Residue 19: TRP, Nonterminal, was not found in name map.) (Residue 20: GLU, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: SER, Nonterminal, was not found in name map.) (Residue 24: PRO, Nonterminal, was not found in name map.) (Residue 25: SER, Nonterminal, was not found in name map.) (Residue 26: THR, Nonterminal, was not found in name map.) (Residue 27: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 28 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 29 to: NGLY. (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: PHE, Nonterminal, was not found in name map.) (Residue 34: HIS, Nonterminal, was not found in name map.) (Residue 35: SER, Nonterminal, was not found in name map.) (Residue 36: PHE, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: VAL, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: ILE, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: CYS, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: GLU, Nonterminal, was not found in name map.) (Residue 47: TRP, Nonterminal, was not found in name map.) (Residue 48: ILE, Nonterminal, was not found in name map.) (Residue 49: GLU, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: TYR, Nonterminal, was not found in name map.) (Residue 52: SER, Nonterminal, was not found in name map.) (Residue 53: PRO, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: THR, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 57 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 58 to: NGLY. (Residue 59: ASP, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: GLY, Nonterminal, was not found in name map.) (Residue 63: LEU, Nonterminal, was not found in name map.) (Residue 64: GLY, Nonterminal, was not found in name map.) (Residue 65: TYR, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: SER, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LEU, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: LYS, Nonterminal, was not found in name map.) (Residue 76: GLY, Nonterminal, was not found in name map.) (Residue 77: TRP, Nonterminal, was not found in name map.) (Residue 78: MET, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: TYR, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: SER, Nonterminal, was not found in name map.) (Residue 84: THR, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 86 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 87 to: NGLY. (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: PHE, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: SER, Nonterminal, was not found in name map.) (Residue 94: ILE, Nonterminal, was not found in name map.) (Residue 95: ILE, Nonterminal, was not found in name map.) (Residue 96: CYS, Nonterminal, was not found in name map.) (Residue 97: LEU, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: GLU, Nonterminal, was not found in name map.) (Residue 100: ILE, Nonterminal, was not found in name map.) (Residue 101: THR, Nonterminal, was not found in name map.) (Residue 102: THR, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: GLY, Nonterminal, was not found in name map.) (Residue 106: TRP, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: TYR, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: SER, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 115 to: CLEU. Joining NGLY - ASP Joining ASP - THR Joining THR - PHE Joining PHE - SER Joining SER - TRP Joining TRP - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ARG Joining ARG - LEU Joining LEU - MET Joining MET - THR Joining THR - GLN Joining GLN - ASP Joining ASP - TYR Joining TYR - TRP Joining TRP - GLU Joining GLU - ASN Joining ASN - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - CLEU Added missing heavy atom: .R<CLEU 71>.A<OXT 20> Added missing heavy atom: .R<CLEU 71>.A<CG 8> Added missing heavy atom: .R<CLEU 71>.A<CD1 10> Added missing heavy atom: .R<CLEU 71>.A<CD2 14> Joining NGLY - ASN Joining ASN - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - HIE Joining HIE - SER Joining SER - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - TRP Joining TRP - ILE Joining ILE - GLU Joining GLU - THR Joining THR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - CLEU Added missing heavy atom: .R<CLEU 100>.A<OXT 20> Added missing heavy atom: .R<CLEU 100>.A<CG 8> Added missing heavy atom: .R<CLEU 100>.A<CD1 10> Added missing heavy atom: .R<CLEU 100>.A<CD2 14> Joining NGLY - ASP Joining ASP - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - THR Joining THR - PHE Joining PHE - LYS Joining LYS - GLY Joining GLY - TRP Joining TRP - MET Joining MET - ASP Joining ASP - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - CLEU Added missing heavy atom: .R<CLEU 129>.A<OXT 20> Added missing heavy atom: .R<CLEU 129>.A<CG 8> Added missing heavy atom: .R<CLEU 129>.A<CD1 10> Added missing heavy atom: .R<CLEU 129>.A<CD2 14> Joining NGLY - GLU Joining GLU - THR Joining THR - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - CYS Joining CYS - LEU Joining LEU - PHE Joining PHE - GLU Joining GLU - ILE Joining ILE - THR Joining THR - THR Joining THR - SER Joining SER - ALA Joining ALA - GLY Joining GLY - TRP Joining TRP - ASP Joining ASP - GLY Joining GLY - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - CLEU Added missing heavy atom: .R<CLEU 158>.A<O 19> Added missing heavy atom: .R<CLEU 158>.A<OXT 20> Added missing heavy atom: .R<CLEU 158>.A<CB 5> Added missing heavy atom: .R<CLEU 158>.A<CG 8> Added missing heavy atom: .R<CLEU 158>.A<CD1 10> Added missing heavy atom: .R<CLEU 158>.A<CD2 14> total atoms in file: 906 Leap added 886 missing atoms according to residue templates: 18 Heavy 868 H / lone pairs > stx = loadmol2 stxagain.mol2 Loading Mol2 file: ./stxagain.mol2 > complex = createunit complex > complex = combine { pore stx } Sequence: Sequence: stx > savepdb complex "c3.pdb" Writing pdb file: c3.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > savepdb stx "stxmin.pdb" Writing pdb file: stxmin.pdb > savepdb pore "pore.pdb" Writing pdb file: pore.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > saveamberparm stx stx.prmtop stx.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.999900 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 c3-c2-nh-hn atoms are: C C7 N5 H5 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N5 N3 C7 N4 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C1 C7 N3 H3 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C2 C3 N HN ** Warning: No sp2 improper torsion term for c3-c3-nh-c2 atoms are: C1 C4 N2 C3 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N N2 C3 N1 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C3 H11 N1 H12 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C7 H41 N4 H42 total 2 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected stx 1 ) (no restraints) > saveamberparm pore pore.prmtop pore.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -8.000000 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 ** 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 394 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. >¥>> # >> # ----- 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" } >> { "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" } >> { "pd" "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: /usr/local/amber8/dat/leap/parm/gaff.dat > > pore = loadpdb "pore_deprotonated.pdb" Loading PDB file: ./pore_deprotonated.pdb 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: THR, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: TRP, Nonterminal, was not found in name map.) (Residue 6: ALA, Nonterminal, was not found in name map.) (Residue 7: PHE, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: PHE, Nonterminal, was not found in name map.) (Residue 12: ARG, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: THR, Nonterminal, was not found in name map.) (Residue 16: GLN, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: TYR, Nonterminal, was not found in name map.) (Residue 19: TRP, Nonterminal, was not found in name map.) (Residue 20: GLU, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: SER, Nonterminal, was not found in name map.) (Residue 24: PRO, Nonterminal, was not found in name map.) (Residue 25: SER, Nonterminal, was not found in name map.) (Residue 26: THR, Nonterminal, was not found in name map.) (Residue 27: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 28 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 29 to: NGLY. (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: PHE, Nonterminal, was not found in name map.) (Residue 34: HIS, Nonterminal, was not found in name map.) (Residue 35: SER, Nonterminal, was not found in name map.) (Residue 36: PHE, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: VAL, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: ILE, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: CYS, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: GLU, Nonterminal, was not found in name map.) (Residue 47: TRP, Nonterminal, was not found in name map.) (Residue 48: ILE, Nonterminal, was not found in name map.) (Residue 49: GLU, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: TYR, Nonterminal, was not found in name map.) (Residue 52: SER, Nonterminal, was not found in name map.) (Residue 53: PRO, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: THR, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 57 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 58 to: NGLY. (Residue 59: ASP, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: GLY, Nonterminal, was not found in name map.) (Residue 63: LEU, Nonterminal, was not found in name map.) (Residue 64: GLY, Nonterminal, was not found in name map.) (Residue 65: TYR, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: SER, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LEU, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: LYS, Nonterminal, was not found in name map.) (Residue 76: GLY, Nonterminal, was not found in name map.) (Residue 77: TRP, Nonterminal, was not found in name map.) (Residue 78: MET, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: TYR, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: SER, Nonterminal, was not found in name map.) (Residue 84: THR, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 86 to: CLEU. Mapped residue GLY, term: Terminal/beginning, seq. number: 87 to: NGLY. (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: PHE, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: SER, Nonterminal, was not found in name map.) (Residue 94: ILE, Nonterminal, was not found in name map.) (Residue 95: ILE, Nonterminal, was not found in name map.) (Residue 96: CYS, Nonterminal, was not found in name map.) (Residue 97: LEU, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: GLU, Nonterminal, was not found in name map.) (Residue 100: ILE, Nonterminal, was not found in name map.) (Residue 101: THR, Nonterminal, was not found in name map.) (Residue 102: THR, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: GLY, Nonterminal, was not found in name map.) (Residue 106: TRP, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: TYR, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: SER, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: PRO, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 115 to: CLEU. Joining NGLY - ASP Joining ASP - THR Joining THR - PHE Joining PHE - SER Joining SER - TRP Joining TRP - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ARG Joining ARG - LEU Joining LEU - MET Joining MET - THR Joining THR - GLN Joining GLN - ASP Joining ASP - TYR Joining TYR - TRP Joining TRP - GLU Joining GLU - ASN Joining ASN - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - ASN Joining ASN - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - HIE Joining HIE - SER Joining SER - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - TRP Joining TRP - ILE Joining ILE - GLU Joining GLU - THR Joining THR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - ASP Joining ASP - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - THR Joining THR - PHE Joining PHE - LYS Joining LYS - GLY Joining GLY - TRP Joining TRP - MET Joining MET - ASP Joining ASP - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Joining NGLY - GLU Joining GLU - THR Joining THR - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - CYS Joining CYS - LEU Joining LEU - PHE Joining PHE - GLU Joining GLU - ILE Joining ILE - THR Joining THR - THR Joining THR - SER Joining SER - ALA Joining ALA - GLY Joining GLY - TRP Joining TRP - ASP Joining ASP - GLY Joining GLY - TYR Joining TYR - SER Joining SER - PRO Joining PRO - SER Joining SER - THR Joining THR - PRO Joining PRO - 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 906 Leap added 886 missing atoms according to residue templates: 18 Heavy 868 H / lone pairs > stx = loadmol2 stxagain.mol2 Loading Mol2 file: ./stxagain.mol2 > complex = createunit complex > complex = combine { pore stx } Sequence: Sequence: stx > savepdb complex "c3.pdb" Writing pdb file: c3.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > savepdb stx "stxmin.pdb" Writing pdb file: stxmin.pdb > savepdb pore "pore.pdb" Writing pdb file: pore.pdb Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU Shortening residue name for PDB format: NGLY -> GLY Shortening residue name for PDB format: CLEU -> LEU > saveamberparm stx stx.prmtop stx.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.999900 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 c3-c2-nh-hn atoms are: C C7 N5 H5 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N5 N3 C7 N4 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C1 C7 N3 H3 ** Warning: No sp2 improper torsion term for c3-c2-nh-hn atoms are: C2 C3 N HN ** Warning: No sp2 improper torsion term for c3-c3-nh-c2 atoms are: C1 C4 N2 C3 ** Warning: No sp2 improper torsion term for nh-nh-c2-nh atoms are: N N2 C3 N1 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C3 H11 N1 H12 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C7 H41 N4 H42 total 2 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected stx 1 ) (no restraints) > saveamberparm pore pore.prmtop pore.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -8.000000 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 ** 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 394 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. 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