#/home/farminf/Programas/PepDice/Examples/outputs/1gab_amber_example04_extended.pdb system = Molecule() name = 'poliALa_from_sequence' TRAJECTORY = name+'_traj' system.name = name system.build_peptide_from_sequence ( sequence = 'AAAAAAAA', _type = 'amber' , force_field = 'ff03ua.labio', overwrite = True , ) system.set_energy_model('RAW') #AAAAAAAA system.import_SS_restraints_from_string ( ss = 'HHHHHHHH', w_ss = '99999999', log= True) print system.compute_SS_energy(log = True) system.energy_components['SS_RESTRAINT'][1] = 100.0 system.energy_components['SIZE' ][1]= 0.0 system.energy_components['CONSTANT' ][1]= 0.0 system.energy_components['ANGLE' ][1]= 0.0 system.energy_components['BOND' ][1]= 0.0 system.energy_components['DIHED' ][1]= 0.0 system.energy_components['EEL' ][1]= 0.0 system.energy_components['EELEC' ][1]= 0.0 system.energy_components['EGB' ][1]= 0.0 system.energy_components['EKtot' ][1]= 0.0 system.energy_components['EPtot' ][1]= 0.0 system.energy_components['ESURF' ][1]= 0.0 system.energy_components['Etot' ][1]= 0.0
#/home/farminf/Programas/PepDice/Examples/outputs/1gab_amber_example04_extended.pdb system = Molecule() name = 'poliALa_1GAB_from_sequence_CMAP_SSrest_restraints' TRAJECTORY = name+'_traj' system.name = name system.build_peptide_from_sequence ( sequence = 'TIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA', _type = 'amber' , force_field = 'ff03ua.labio', overwrite = True , ) system.set_energy_model('RAW') #AAAAAAAA system.import_SS_restraints_from_string ( ss = 'CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC', w_ss = '00023456788888654320000000034565400000023456789654000', log= True) print system.compute_SS_energy(log = True) system.energy_components['SS_RESTRAINT'] [1]= 1.0 system.energy_components['SIZE' ][1]= 0.0 system.energy_components['CONSTANT' ][1]= 0.0 system.energy_components['ANGLE' ][1]= 0.0 system.energy_components['BOND' ][1]= 0.0 system.energy_components['DIHED' ][1]= 0.0 system.energy_components['EEL' ][1]= 0.0 system.energy_components['EELEC' ][1]= 0.0 system.energy_components['EGB' ][1]= 0.0 system.energy_components['EKtot' ][1]= 0.0 system.energy_components['EPtot' ][1]= 0.0 system.energy_components['ESURF' ][1]= 0.0 system.energy_components['Etot' ][1]= 0.0
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1GAB/1GAB_A_AMBER_minimized.pdb' ) ) system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1GAB/1GAB_A_AMBER.top') , torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') ) print system.compute_R_gy_Calpha() #print system.compute_SS_energy(log = True) #cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True) #system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER_minimized.pdb') ) #system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER.top') , # torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') ) # system.import_SS_restraints_from_string ( ss = 'CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC', w_ss = '00000123345553221111000000001234432100012342335556110', log= True) print system.compute_SS_energy(log = True) #restraint = { # 'Kd' : 40.0, # 'resi_i' : 1 , #starts at ZERO # 'resi_j' : 5 , # 'atom_name_i' : 'CA', # 'atom_name_j' : 'CA', # 'distance' : 10.0, # } # #system.hamonical_potential_restraint_list.append(restraint) print system.compute_harmonical_restraint_energies(log = True)