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: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 = 'aminoacids3:AceAlaNme'
# amber96_tip3p_octahedral_14.prmtop and amber96_tip3p_octahedral_14.inpcrd
output=['amber96_tip3p_octahedral_14.prmtop', 'amber96_tip3p_octahedral_14.inpcrd']
print("{} and {}... ".format(output[0], output[1]), end =" ")
msm.build_peptide(sequence, forcefield='AMBER96', water_model='TIP3P', box_geometry='truncated_octahedral',
clearance=14*unit.angstroms, to_form=output, verbose=False)
msm.energy_minimization(output, forcefield='AMBER96', water_model='TIP3P', to_form=output[1], verbose=False)
print("done")
# amber14_tip3p_octahedral_14.prmtop and amber14_tip3p_octahedral_14.inpcrd
output=['amber14_tip3p_octahedral_14.prmtop', 'amber14_tip3p_octahedral_14.inpcrd']
print("{} and {}... ".format(output[0], output[1]), end =" ")
msm.build_peptide(sequence, forcefield='AMBER14', water_model='TIP3P', box_geometry='truncated_octahedral',
clearance=14*unit.angstroms, to_form=output, verbose=False)
msm.energy_minimization(output, forcefield='AMBER14', water_model='TIP3P', to_form=output[1], verbose=False)
print("done")
# octahedral_14.pdb
output='octahedral_14.pdb'
print("{}... ".format(output, end =" "))
tmp_item = msm.build_peptide(sequence, forcefield='AMBER14', water_model='TIP3P', box_geometry='truncated_octahedral',
clearance=14*unit.angstroms, to_form='openmm.Modeller', verbose=False)
msm.energy_minimization(output, forcefield='AMBER14', water_model='TIP3P', to_form=output, verbose=False)
print("done")