log started: Thu Jul 7 18:16:23 2011 Log file: ./leapante.log > addAtomTypes { > { "nh" "N" "sp3" } > { "c" "C" "sp2" } > { "n3" "N" "sp3" } > { "hn" "H" "sp3" } > { "oh" "O" "sp3" } > { "cc" "C" "sp2" } > { "na" "N" "sp2" } > { "ca" "C" "sp2" } > { "nc" "N" "sp2" } > { "o" "O" "sp2" } > { "n" "N" "sp2" } > { "cl" "Cl" "sp3" } > { "ss" "S" "sp2" } > { "ha" "H" "sp3" } > { "h4" "H" "sp3" } > { "c3" "C" "sp3" } > { "hc" "H" "sp3" } > { "cd" "C" "sp2" } > { "nb" "N" "sp2" } > { "h1" "H" "sp3" } > { "ho" "H" "sp3" } > } > ligfrc = loadAmberParams ante_dasatinib.gaff.frcmod Loading parameters: ./ante_dasatinib.gaff.frcmod Reading force field modification type file (frcmod) Reading title: Antechamber frcmod file generated for dasatinib.gaff.mol2 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: c3 ca ca ca 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca ha 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca cl 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca n 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca c n hn 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: n cc c o 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: c ss cc cd 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: cc nc cd h4 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nc ss cc nh 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: cc ca nh hn 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nh na ca ca 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca nb ca nh 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nb na ca c3 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca na hn 0.000 180.000 2.000 *Antechamber_generated* > lig = loadMol2 dasatinib.gaff_pchk.mol2 Loading Mol2 file: ./dasatinib.gaff_pchk.mol2 Reading MOLECULE named ZINC21982951 > > complex = { protein lig } > > # Specify disulfide bonds, if present. > > # Check protein. > check complex check: Argument #1 is type List must be of type: [unit molecule residue atom] usage: check [parmset] > > # Write protein parameters. > saveAmberParm complex complex.prmtop complex.crd saveAmberParm: Argument #1 is type List must be of type: [unit] usage: saveAmberParm > > complex ERROR: syntax error > check complex check: Argument #1 is type List must be of type: [unit molecule residue atom] usage: check [parmset] > complex = combine { protein lig } Sequence: Sequence: ZINC21982951 > quit Quit log started: Thu Jul 7 18:17:18 2011 Log file: ./leapante.log > addAtomTypes { > { "nh" "N" "sp3" } > { "c" "C" "sp2" } > { "n3" "N" "sp3" } > { "hn" "H" "sp3" } > { "oh" "O" "sp3" } > { "cc" "C" "sp2" } > { "na" "N" "sp2" } > { "ca" "C" "sp2" } > { "nc" "N" "sp2" } > { "o" "O" "sp2" } > { "n" "N" "sp2" } > { "cl" "Cl" "sp3" } > { "ss" "S" "sp2" } > { "ha" "H" "sp3" } > { "h4" "H" "sp3" } > { "c3" "C" "sp3" } > { "hc" "H" "sp3" } > { "cd" "C" "sp2" } > { "nb" "N" "sp2" } > { "h1" "H" "sp3" } > { "ho" "H" "sp3" } > } > ligfrc = loadAmberParams ante_dasatinib.gaff.frcmod Loading parameters: ./ante_dasatinib.gaff.frcmod Reading force field modification type file (frcmod) Reading title: Antechamber frcmod file generated for dasatinib.gaff.mol2 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: c3 ca ca ca 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca ha 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca cl 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca ca n 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca c n hn 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: n cc c o 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: c ss cc cd 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: cc nc cd h4 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nc ss cc nh 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: cc ca nh hn 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nh na ca ca 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca nb ca nh 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: nb na ca c3 0.000 180.000 2.000 *Antechamber_generated* WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: ca ca na hn 0.000 180.000 2.000 *Antechamber_generated* > lig = loadMol2 dasatinib.gaff_pchk.mol2 Loading Mol2 file: ./dasatinib.gaff_pchk.mol2 Reading MOLECULE named ZINC21982951 > > complex = combine { protein lig } Sequence: Sequence: ZINC21982951 > > # Specify disulfide bonds, if present. > > # Check protein. > check complex Checking 'complex'.... WARNING: The unperturbed charge of the unit: -6.000200 is not zero. Checking parameters for unit 'complex'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 1 Unit is OK. > > # Write protein parameters. > saveAmberParm complex complex.prmtop complex.crd Checking Unit. WARNING: The unperturbed charge of the unit: -6.000200 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 ** Warning: No sp2 improper torsion term for ca-c3-nh-c3 atoms are: C14 C20 N6 C17 total 493 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 CLEU 1 NALA 1 ZINC21982951 1 ) (no restraints) > > quit Quit