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
system.energy_components['EEL' ][1]= 0.0
system.energy_components['EELEC' ][1]= 0.0
system.energy_components['EGB' ][1]= 0.0
#-------------------------------------------------------------------------------
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()
system.build_peptide_from_sequence (
sequence = 'AADD',
_type = 'amber' ,
force_field = 'ff03ua.labio',
overwrite = True ,
)
system.set_energy_model('FULL')
#system.energy(log = True)
hydropathic_table_AB = {
'ARG' : 'B', #-4.5,
'LYS' : 'B', #-3.9,
'ASN' : 'B', #-3.5,
'ASP' : 'B', #-3.5,
'GLU' : 'B', #-3.5,
'GLN' : 'B', #-3.5,
'HIS' : 'B', #-3.2,
'HIE' : 'B', #-3.2,
'PRO' : 'B', #-1.6,
# 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)
#-------------------------------------------------------------------------------
# creating a new system
system = Molecule()
system.name = '1I6C - LABIO dataset'
# - setup energy model
system.set_energy_model('amber')
# importing coordinates and amber parameters
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_A_AMBER_minimized.pdb' ) )
system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_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') )
#
#-------------------------------------------------------------------------------
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,
ntr = 0)
save_PDB_to_file(system, '03_estendida_A_AMBER_minimized.pdb')
