amber.set14Factors(0,0)
print("Loading protein box with zero 1-4 factors...")
if os.path.exists("../io/proteinbox_zero14.s3"):
(mols, space) = Sire.Stream.load("../io/proteinbox_zero14.s3")
else:
(mols,space) = amber.readCrdTop("../io/proteinbox.crd", "../io/proteinbox.top")
Sire.Stream.save( (mols,space), "../io/proteinbox_zero14.s3" )
#space = Cartesian()
protein = mols[ MolWithResID("ALA") ].molecule()
ligand = mols[ MolWithResID("OSE") ].molecule()
flex = AmberLoader.generateFlexibility(ligand)
ligand = ligand.edit().setProperty("flexibility", flex).commit()
oldff = IntraCLJFF("oldff")
oldff.setSwitchingFunction(switchfunc)
oldff.setSpace(space)
oldff.setShiftElectrostatics(True)
newff = IntraFF("newff")
newff.setProperty("cljFunction", CLJIntraShiftFunction())
newff.setProperty("switchingFunction",switchfunc)
newff.setProperty("space",space)
newff.disableParallelCalculation()
parff = IntraFF("parff")
parff.setProperty("cljFunction", CLJIntraShiftFunction())
params = {}
params["bond flex"] = max_delta_bond
params["angle flex"] = max_delta_angle
params["dihedral flex"] = max_delta_dihedral
params["h dihedral flex"] = max_delta_dihedral
params["maxvar"] = max_num_move
Parameter.push(params)
# Load the molecules and the periodic box from the crd/top files
(mols, space) = Amber().readCrdTop("l7n.crd", "l7n.top")
# extract the ligand molecule (molecule with residue called "L7N")
ligand_mol = mols[ MolWithResID("L7N") ].molecule()
# auto-generate the flexibility for the ligand
flexibility = AmberLoader.generateFlexibility(ligand_mol)
# attach this flexibility to the ligand using the 'flexibility' property
ligand_mol = ligand_mol.edit() \
.setProperty("flexibility", flexibility) \
.commit()
mols.update(ligand_mol)
# extract the protein molecule (molecule with residue called "ALA")
protein_mol = mols[ MolWithResID("ALA") ].molecule()
# auto-generate the z-matrix for the protein
zmat_maker = ZmatrixMaker()
zmat_maker.loadTemplates( os.path.join(parameter_directory, "amber.zmatrices") )
protein_mol = zmat_maker.applyTemplates(protein_mol)
from Sire.Tools import AmberLoader
from Sire.Tools import Parameter
from Sire.IO import *
params = {}
params["water model"] = "tip4p"
Parameter.push(params)
watersys = AmberLoader.createSystem("test/io/waterbox.top",
"test/io/waterbox.crd")
PDB().write(watersys.molecules(), "test_tip4p.pdb")
params = {}
params["bond flex"] = max_delta_bond
params["angle flex"] = max_delta_angle
params["dihedral flex"] = max_delta_dihedral
params["h dihedral flex"] = max_delta_dihedral
params["maxvar"] = max_num_move
Parameter.push(params)
# Load the molecules and the periodic box from the crd/top files
(mols, space) = Amber().readCrdTop("l7n.crd", "l7n.top")
# extract the ligand molecule (molecule with residue called "L7N")
ligand_mol = mols[MolWithResID("L7N")].molecule()
# auto-generate the flexibility for the ligand
flexibility = AmberLoader.generateFlexibility(ligand_mol)
# attach this flexibility to the ligand using the 'flexibility' property
ligand_mol = ligand_mol.edit() \
.setProperty("flexibility", flexibility) \
.commit()
mols.update(ligand_mol)
# extract the protein molecule (molecule with residue called "ALA")
protein_mol = mols[MolWithResID("ALA")].molecule()
# auto-generate the z-matrix for the protein
zmat_maker = ZmatrixMaker()
zmat_maker.loadTemplates(os.path.join(parameter_directory, "amber.zmatrices"))
protein_mol = zmat_maker.applyTemplates(protein_mol)
from Sire.Tools import AmberLoader
from Sire.Tools import Parameter
from Sire.IO import *
params = {}
params["water model"] = "tip4p"
Parameter.push(params)
watersys = AmberLoader.createSystem("test/io/waterbox.top", "test/io/waterbox.crd")
PDB().write(watersys.molecules(), "test_tip4p.pdb")