porgasem@porgasem-desktop ~/Desktop/amber $ tleap -f leaprc.ff99SB -I: Adding /home/porgasem/amber12/dat/leap/prep to search path. -I: Adding /home/porgasem/amber12/dat/leap/lib to search path. -I: Adding /home/porgasem/amber12/dat/leap/parm to search path. -I: Adding /home/porgasem/amber12/dat/leap/cmd to search path. -f: Source leaprc.ff99SB. Welcome to LEaP! (no leaprc in search path) Sourcing: /home/porgasem/amber12/dat/leap/cmd/leaprc.ff99SB Log file: ./leap.log Loading parameters: /home/porgasem/amber12/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/porgasem/amber12/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/porgasem/amber12/dat/leap/lib/all_nucleic94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_amino94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_aminoct94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_aminont94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/ions94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/solvents.lib > protein = loadpdb protein.pdb Loading PDB file: ./protein.pdb Added missing heavy atom: .R.A total atoms in file: 1745 Leap added 1741 missing atoms according to residue templates: 1 Heavy 1740 H / lone pairs > saveamberparm protein protein.prmtop protein.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -3.000000 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. total 710 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 CHIE 1 NPRO 1 ) (no restraints) > source leaprc.ff99SB ----- Source: /home/porgasem/amber12/dat/leap/cmd/leaprc.ff99SB ----- Source of /home/porgasem/amber12/dat/leap/cmd/leaprc.ff99SB done Log file: ./leap.log Loading parameters: /home/porgasem/amber12/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/porgasem/amber12/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/porgasem/amber12/dat/leap/lib/all_nucleic94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_amino94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_aminoct94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/all_aminont94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/ions94.lib Loading library: /home/porgasem/amber12/dat/leap/lib/solvents.lib Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT Substituting map 0G -> RG5 for 0G -> RG5 Substituting map 1G -> RG3 for 1G -> RG3 Substituting map G -> RG for G -> RG Substituting map GN -> RGN for GN -> RGN Substituting map 0A -> RA5 for 0A -> RA5 Substituting map 1A -> RA3 for 1A -> RA3 Substituting map A -> RA for A -> RA Substituting map AN -> RAN for AN -> RAN Substituting map 0C -> RC5 for 0C -> RC5 Substituting map 1C -> RC3 for 1C -> RC3 Substituting map C -> RC for C -> RC Substituting map CN -> RCN for CN -> RCN Substituting map 0U -> RU5 for 0U -> RU5 Substituting map 1U -> RU3 for 1U -> RU3 Substituting map U -> RU for U -> RU Substituting map UN -> RUN for UN -> RUN Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map O2* -> O2' for O2* -> O2' Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2'1 for H2*1 -> H2'1 Substituting map H2*2 -> H2'2 for H2*2 -> H2'2 Substituting map H2' -> H2'1 for H2' -> H2'1 Substituting map H2'' -> H2'2 for H2'' -> H2'2 Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5'1 for H5*1 -> H5'1 Substituting map H5*2 -> H5'2 for H5*2 -> H5'2 Substituting map H5' -> H5'1 for H5' -> H5'1 Substituting map H5'' -> H5'2 for H5'' -> H5'2 Substituting map HO2' -> HO'2 for HO2' -> HO'2 Substituting map HO5' -> H5T for HO5' -> H5T Substituting map HO3' -> H3T for HO3' -> H3T Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> O1P for OA -> O1P Substituting map OB -> O2P for OB -> O2P Substituting map OP1 -> O1P for OP1 -> O1P Substituting map OP2 -> O2P for OP2 -> O2P > LIG = loadmol2 LIG.mol2 Loading Mol2 file: ./LIG.mol2 Reading MOLECULE named MOL > loadamberparams LIG.frcmod Loading parameters: ./LIG.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > saveoff LIG LIG.lib Building topology. Building atom parameters. > loadoff LIG.lib Loading library: ./LIG.lib > check LIG Checking 'LIG'.... WARNING: The unperturbed charge of the unit: -2.000000 is not zero. Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 1 Unit is OK. > saveamberparm LIG LIG.prmtop LIG.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. total 26 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 MOL 1 ) (no restraints) > complex = loadpdb complex.pdb Loading PDB file: ./complex.pdb Unknown residue: HEM number: 214 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Added missing heavy atom: .R.A Creating new UNIT for residue: HEM sequence: 224 Created a new atom named: Fe1 within residue: .R Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: C7 within residue: .R Created a new atom named: C8 within residue: .R Created a new atom named: C9 within residue: .R Created a new atom named: C10 within residue: .R Created a new atom named: C11 within residue: .R Created a new atom named: C12 within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N2 within residue: .R Created a new atom named: C13 within residue: .R Created a new atom named: C14 within residue: .R Created a new atom named: C15 within residue: .R Created a new atom named: C16 within residue: .R Created a new atom named: C17 within residue: .R Created a new atom named: C18 within residue: .R Created a new atom named: C19 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C20 within residue: .R Created a new atom named: C21 within residue: .R Created a new atom named: C22 within residue: .R Created a new atom named: C23 within residue: .R Created a new atom named: C24 within residue: .R Created a new atom named: C25 within residue: .R Created a new atom named: C26 within residue: .R Created a new atom named: N4 within residue: .R Created a new atom named: C27 within residue: .R Created a new atom named: C28 within residue: .R Created a new atom named: C29 within residue: .R Created a new atom named: C30 within residue: .R Created a new atom named: C31 within residue: .R Created a new atom named: C32 within residue: .R Created a new atom named: C33 within residue: .R Created a new atom named: C34 within residue: .R Created a new atom named: O3 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: H1 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H4 within residue: .R Created a new atom named: H5 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: H12 within residue: .R Created a new atom named: H13 within residue: .R Created a new atom named: H14 within residue: .R Created a new atom named: H15 within residue: .R Created a new atom named: H16 within residue: .R Created a new atom named: H17 within residue: .R Created a new atom named: H18 within residue: .R Created a new atom named: H19 within residue: .R Created a new atom named: H20 within residue: .R Created a new atom named: H21 within residue: .R Created a new atom named: H22 within residue: .R Created a new atom named: H23 within residue: .R Created a new atom named: H24 within residue: .R Created a new atom named: H25 within residue: .R Created a new atom named: H26 within residue: .R Created a new atom named: H27 within residue: .R Created a new atom named: H28 within residue: .R Created a new atom named: H29 within residue: .R Created a new atom named: H30 within residue: .R total atoms in file: 1818 Leap added 1741 missing atoms according to residue templates: 1 Heavy 1740 H / lone pairs The file contained 73 atoms not in residue templates