restraint = {'resi_i' : 20 , 'atom_name_i' : 'CA', 'resi_j' : 48 , 'atom_name_j' : 'CA', 'distance' : 11.2, 'Kd' : 1.0 , } system.hamonical_potential_restraint_list.append(restraint) system.Status() i = system.energy() ''' minimize( molecule=system, imin = 1, maxcyc=1000, ncyc = 100, cut = 10, rgbmax= 999, igb = 1, ntb = 0, ntpr = 100, ntr = 0) ''' save_PDB_to_file(system, '03_estendida_A_AMBER_minimized.pdb')
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') ) # energy_models = ['LABIO']#, 'FULL', 'iLABIO'] for model in energy_models: system.set_energy_model(model) #system.energy_model_parameters['saltcon'] = 1.0 #system.energy_model_parameters['surften'] = 1.0 #system.energy_model_parameters['igb'] = 1 #if model == 'Contact': system.import_CMAP(cmap = cmap) system.Status() system.energy( log =True) #print 'energy:', model ,system.energy() print '\n\n\n'
energy_models = ['LABIO'] energies = [ ] print '%-35s%8s %15s %15s %15s %15s %15s %15s %15s %15s %15s %15s %15s %15s' %( 'decoy','RMSD','CONTACT','R_GYRATION', 'AB_ENERGY','ANGLE','BOND','DIHED','EEL','EELEC','EGB','ESURF','NB','VDWAALS') # decoy13_122_A_AMBER_minimized.pdb 8.0900 8953.8127000 335.8717000 374.7391660 0.4041721 for decoy in decoys: text = '%-35s %8.4f' %(decoy, decoys[decoy]) system.load_PDB_to_system (filename = os.path.join(folder, decoy)) system.import_CMAP(cmap = cmap) energy_list = system.energy(return_list =True) text += '%15.7f ' %(energy_list['CONTACT']) text += '%15.7f ' %(energy_list['R_GYRATION']) text += '%15.7f ' %(energy_list['AB_ENERGY']) text += '%15.7f ' %(energy_list['ANGLE' ]) text += '%15.7f ' %(energy_list['BOND' ]) text += '%15.7f ' %(energy_list['DIHED' ]) text += '%15.7f ' %(energy_list['EEL' ]) text += '%15.7f ' %(energy_list['EELEC' ]) text += '%15.7f ' %(energy_list['EGB' ]) text += '%15.7f ' %(energy_list['ESURF' ]) text += '%15.7f ' %(energy_list['NB' ]) text += '%15.7f ' %(energy_list['VDWAALS' ])
contacts = [] #saltcon = 0.00 #EGBs = [] # #for i in range(0, 6): # # system.energy_model_parameters['saltcon'] = saltcon # energies = system.energy(return_list = True) # saltcon += 0.1 # EGBs.append(energies['EGB']) #energies = system.energy(return_list = True) system.set_energy_model('LABIO') energy = system.energy() system.set_energy_model('FULL') energy2 = system.energy() #for i in range (0, 6): # cmap = CMAP(pdb = 'native_A_AMBER_minimized.pdb', cutoff = cutoff, log = False) # system.import_CMAP(cmap = cmap) # contact = system.compute_CONTACT_energy() # contacts.append(contact) # cutoff += 0.5 #print folder #print contacts
for pdb in RMSD_list: if pdb == 'NAME': pass else: filename = pdb.replace('.', '_A_AMBER_minimized.') system.load_PDB_to_system (filename = filename) system.set_energy_model('FULL') #pprint(RMSD_list) system.import_CMAP(cmap = cmap) try: energies = system.energy(return_list = True) text = '%-20s %-10s %6s %6d %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f %15.7f' %( pdb , folder , RMSD_list[pdb] , len(system.residues) , energies['AB_ENERGY'], energies['CONTACT' ], energies['ANGLE' ], energies['BOND' ], energies['DIHED' ], energies['EEL' ], energies['EELEC' ], energies['EGB' ],