# building a contact map - required for Contact model calculations #------------------------------------------------------------------------------- #from CMAP import CMAP #cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True) #------------------------------------------------------------------------------- PDB = '1GAB' sequence = 'TIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA' # creating a new system system = Molecule() system.name = PDB+'-from_sequence' system.build_peptide_from_sequence ( sequence = sequence, _type = 'amber' , force_field = 'ff03ua.labio', overwrite = True , ) system.set_energy_model('RAW') minimize(molecule = system, imin = 1 , maxcyc= 1000 , ncyc = 100 , cut = 10 , rgbmax= 999 , igb = 1 , ntb = 0 , ntpr = 100 , ntr = 0 )
#------------------------------------------------------------------------------- PEPDICE = os.environ.get('PEPDICE') PEPDICE_EXAMPLES = os.path.join(PEPDICE, 'Examples') PEPDICE_PARAMETER= os.path.join(PEPDICE, 'Parameters') #------------------------------------------------------------------------------- #/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
#----------------------------------------------------# import random random.seed(1234) #------------------------------------------------------------------------------- PEPDICE = os.environ.get('PEPDICE') PEPDICE_EXAMPLES = os.path.join(PEPDICE, 'Examples') PEPDICE_PARAMETER= os.path.join(PEPDICE, 'Parameters') #------------------------------------------------------------------------------- #/home/farminf/Programas/PepDice/Examples/outputs/1gab_amber_example04_extended.pdb system = Molecule() system.build_peptide_from_sequence ( sequence = 'KLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNSSSG', _type = 'amber' , force_field = 'ff03ua.labio', overwrite = True , ) system.set_energy_model('iLABIO') ''' minimize( molecule=system, imin = 1, maxcyc=1000, ncyc = 100, cut = 10, rgbmax= 999, igb = 1, ntb = 0, ntpr = 100,