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")