log started: Sun Apr 2 09:06:30 2006 Log file: ./LEaP-Tutorial-1.log > > verbosity 2 Verbosity level: 2 > > # Load the two Tripos mol2 file > ALPHA = loadmol2 4-Charges-2conf-RBRA-4/Mol_m1-o1.mol2 Loading Mol2 file: ./4-Charges-2conf-RBRA-4/Mol_m1-o1.mol2 > BETA = loadmol2 4-Charges-2conf-RBRA-4/Mol_m1-o2.mol2 Loading Mol2 file: ./4-Charges-2conf-RBRA-4/Mol_m1-o2.mol2 > # Calculate the total charge of ALPHA and BETA > charge ALPHA Total unperturbed charge: -0.000200 Total perturbed charge: -0.000200 > charge BETA Total unperturbed charge: -0.000200 Total perturbed charge: -0.000200 > > # set general information > set ALPHA name "ALPHA" > set ALPHA.1 restype protein > set ALPHA.2 restype protein > set ALPHA.3 restype protein > set ALPHA.1 name "ACE" > set ALPHA.2 name "AIB" > set ALPHA.3 name "NME" > # set FF atom types for ACE > set ALPHA.1.C1 type CT > set ALPHA.1.H11 type HC > set ALPHA.1.H12 type HC > set ALPHA.1.H13 type HC > set ALPHA.1.C type C > set ALPHA.1.O type O > # set FF atom types for ACE > set ALPHA.2.N type N > set ALPHA.2.H type H > set ALPHA.2.CA type CT > set ALPHA.2.CB1 type CT > set ALPHA.2.HB11 type HC > set ALPHA.2.HB12 type HC > set ALPHA.2.HB13 type HC > set ALPHA.2.CB2 type CT > set ALPHA.2.HB21 type HC > set ALPHA.2.HB22 type HC > set ALPHA.2.HB23 type HC > set ALPHA.2.C type C > set ALPHA.2.O type O > # set FF atom types for NME > set ALPHA.3.N type N > set ALPHA.3.H type H > set ALPHA.3.C2 type CT > set ALPHA.3.H21 type H1 > set ALPHA.3.H22 type H1 > set ALPHA.3.H23 type H1 > # save the OFF library > saveoff ALPHA ALPHA.off Creating ALPHA.off Saving ALPHA. Building topology. Building atom parameters. > # quit >