Exemplo n.º 1
0
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")
Exemplo n.º 2
0
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',
Exemplo n.º 3
0
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")