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)