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' ],
