import molsysmt as msm import simtk.unit as unit sequence = 'aminoacids3:AceAlaNme' # amber96_gbsaobc.prmtop and amber96_gbsaobc.inpcrd output = ['amber96_gbsaobc.prmtop', 'amber96_gbsaobc.inpcrd'] print("{} and {}... ".format(output[0], output[1]), end=" ") msm.build_peptide(sequence, forcefield='AMBER96', implicit_solvent='OBC1', to_form=output, verbose=False) msm.energy_minimization(output, forcefield='AMBER96', implicit_solvent='OBC1', to_form=output[1], verbose=False) print("done") # amber14_gbsaobc.prmtop and amber14_gbsaobc.inpcrd output = ['amber14_gbsaobc.prmtop', 'amber14_gbsaobc.inpcrd'] print("{} and {}... ".format(output[0], output[1]), end=" ") msm.build_peptide(sequence, forcefield='AMBER14', implicit_solvent='OBC1', to_form=output, verbose=False) msm.energy_minimization(output, forcefield='AMBER14', implicit_solvent='OBC1',
import molsysmt as msm import simtk.unit as unit sequence = 'TyrGlyGlyPheMet' # vacuum.pdb output='vacuum.pdb' print("{}... ".format(output), end =" ") tmp_item = msm.build_peptide(sequence, forcefield='AMBER14', to_form='openmm.Modeller', verbose=False) msm.terminal_capping(tmp_item) msm.energy_minimization(tmp_item, forcefield='AMBER14', to_form=output, verbose=False) print("done") # octahedral_14.pdb output='octahedral_14.pdb' print("{}... ".format(output, end =" ")) msm.solvate('vacuum.pdb', box_geometry="truncated_octahedral", clearance=14.0*unit.angstroms, water_model='TIP3P', anion='Cl-', num_anions="neutralize", cation='Na+', num_cations="neutralize", 18 ionic_strength= 0.0*unit.molar, forcefield='AMBER14', engine="LEaP", 19 to_form= None, logfile=False, verbose=False): ) msm.build_peptide(sequence, forcefield='AMBER14', water_model='TIP3P', box_geometry='truncated_octahedral', clearance=14*unit.angstroms, to_form=output, verbose=False) print("done")
import molsysmt as msm import simtk.unit as unit sequence = 'aminoacids3:AceAlaNme' # vacuum.pdb output = 'vacuum.pdb' print("{}... ".format(output), end=" ") tmp_item = msm.build_peptide(sequence, forcefield='AMBER96', to_form='openmm.Modeller', verbose=False) msm.energy_minimization(tmp_item, forcefield='AMBER96', to_form=output, verbose=False) print("done")
import molsysmt as msm import simtk.unit as unit sequence = 'aminoacids3:AceAlaAlaAlaNme' # vacuum.pdb output = 'vacuum.pdb' print("{}... ".format(output), end=" ") tmp_item = msm.build_peptide(sequence, forcefield='AMBER14', to_form='openmm.Modeller', verbose=False) msm.energy_minimization(tmp_item, forcefield='AMBER14', to_form=output, verbose=False) print("done") # octahedral_14.pdb output = 'octahedral_14.pdb' print("{}... ".format(output, end=" ")) msm.build_peptide(sequence, forcefield='AMBER14', water_model='TIP3P', box_geometry='truncated_octahedral', clearance=14 * unit.angstroms, to_form=output, verbose=False) print("done")