Ejemplo n.º 1
0
def test_charmm22star_1lyd():
    subprocess.check_output('viparr 1LYD.pdb 1LYD.dms -f charmm22star_aminoacids --without-constraints', shell=True)
    dms = DesmondDMSFile('1LYD.dms')
    system1 = dms.createSystem()
    context1 = mm.Context(system1, mm.VerletIntegrator(0))
    context1.setPositions(dms.positions)
    state1 = context1.getState(getForces=True)
    force1 = state1.getForces(asNumpy=True)

    print force1
Ejemplo n.º 2
0
def test_amber99_no_constraints():
    subprocess.check_output('viparr ala2.pdb ala2.dms -f amber99SB-ILDN --without-constraints', shell=True)
    dms = DesmondDMSFile('ala2.dms')
    system1 = dms.createSystem()
    context1 = mm.Context(system1, mm.VerletIntegrator(0))
    context1.setPositions(dms.positions)
    state1 = context1.getState(getForces=True)
    force1 = state1.getForces(asNumpy=True)

    pdb = app.PDBFile('ala2.pdb')
    forcefield = app.ForceField('amber99sbildn.xml')
    system2 = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=None)
    context2 = mm.Context(system2, mm.VerletIntegrator(0))
    context2.setPositions(pdb.getPositions())
    state2 = context2.getState(getForces=True)
    force2 = state2.getForces(asNumpy=True)

    np.testing.assert_array_almost_equal(np.array(force1), np.array(force2), decimal=1)
Ejemplo n.º 3
0
def test_1plx():
    subprocess.check_output('pdb2gmx -f 1PLX.pdb -ff charmm22star -ignh -water tip3p', shell=True)
    gro = app.GromacsGroFile('conf.gro')
    top = app.GromacsTopFile('topol.top')
    app.PDBFile.writeFile(top.topology, gro.positions, open('temp.pdb', 'w'))
    subprocess.check_output('viparr temp.pdb temp.dms -f charmm22star_aminoacids --without-constraints', shell=True)
    dms = DesmondDMSFile('temp.dms')
    system1 = dms.createSystem()
    context1 = mm.Context(system1, mm.VerletIntegrator(0))

    context1.setPositions(dms.positions)
    state1 = context1.getState(getForces=True)
    force1 = np.array(state1.getForces(asNumpy=True))


    system2 = top.createSystem(nonbondedMethod=app.NoCutoff, constraints=None)
    context2 = mm.Context(system2, mm.VerletIntegrator(0))
    context2.setPositions(gro.getPositions())
    state2 = context2.getState(getForces=True)
    force2 = np.array(state2.getForces(asNumpy=True))

    np.testing.assert_array_almost_equal(np.array(force1), np.array(force2), decimal=1)