log started: Fri Apr 13 18:32:41 2012 Log file: ./leap.log > # > # ----- leaprc for loading the ff12SB force field > # ----- NOTE: this is designed for PDB format 3! > # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "Cs+" "Cs" "sp3" } > { "Mg+" "Mg" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm10 = loadamberparams parm10.dat Loading parameters: /Users/genzotanaka/Downloads/amber12/dat/leap/parm/parm10.dat Loading parameters: /Users/genzotanaka/Downloads/amber12/dat/leap/parm/frcmod.ff12SB Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/amino12.lib > loadOff aminoct12.lib Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/aminoct12.lib > loadOff aminont12.lib Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/aminont12.lib > loadOff nucleic12.lib Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/nucleic12.lib > loadOff ions08.lib Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /Users/genzotanaka/Downloads/amber12/dat/leap/lib/solvents.lib > # > # Define the PDB name map for the amino acids and nucleic acids > # > addPdbResMap { > } > > # try to be good about reading in really old atom names as well: > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } . . . > { "OB" "OP2" } > { "O1P" "OP1" } > { "O2P" "OP2" } > } > > # > # assume that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > loadamberparams lingwang.dat Loading parameters: ./lingwang.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for LING > loadamberparams /Users/genzotanaka/Downloads/amber12/dat/leap/parm/parm10.dat Loading parameters: /Users/genzotanaka/Downloads/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > loadoff CHN0.lib Loading library: ./CHN0.lib Loading: CHN0 > edit CHN0 Unit Editor: > check CHN0 Unit Editor: Checking 'CHN0'.... Unit Editor: Warning: Close contact of 0.654270 angstroms between .R.A and .R.A Unit Editor: Checking parameters for unit 'CHN0'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: check: Warnings: 1 Unit Editor: Unit is OK. Unit Editor: (used 12 default torsion params) Unit Editor: Gradient RMS=69.166936 Unit Editor: Gradient RMS=4.159068 Unit Editor: Gradient RMS=1.152176 Unit Editor: Gradient RMS=0.290488 Unit Editor: Gradient RMS=0.125914 Unit Editor: Gradient RMS=0.081189 Unit Editor: Gradient RMS=0.054874 Unit Editor: Gradient RMS=0.028071 Unit Editor: Search terminated when RMS gradient became small enough! Unit Editor: Number of conjugate gradient steps taken: 72 Unit Editor: > check CHN0 Unit Editor: Checking 'CHN0'.... Unit Editor: Warning: Close contact of 0.629348 angstroms between .R.A and .R.A Unit Editor: Checking parameters for unit 'CHN0'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: check: Warnings: 1 Unit Editor: Unit is OK. > saveOFF CHN0 CHN0.lib Saving CHN0. Building topology. Building atom parameters. > saveamberparm CHN0 CHN0.top CHN0.crd Checking Unit. Building topology. Building atom parameters. For atom: .R.A Could not find type: F For atom: .R.A Could not find type: F For atom: .R.A Could not find type: F Parameter file was not saved. Table Editor: Check table... Table Editor: The table has no errors and 0 warnings. Table Editor: Table has been 'saved' back to the program. > saveOFF CHN0 CHN0.lib Saving CHN0. Building topology. Building atom parameters. > saveamberparm CHN0 CHN0.top CHN0.crd Checking Unit. Building topology. Building atom parameters. For atom: .R.A Could not find type: F For atom: .R.A Could not find type: F For atom: .R.A Could not find type: F Parameter file was not saved.