diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
new file mode 100644
index 0000000000000000000000000000000000000000..641b5e16817d19dc9d4fb4fea5d125174fb7835d
--- /dev/null
+++ b/modules/mol/mm/doc/integrators.rst
@@ -0,0 +1,125 @@
+Integrators
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The Integrators are a wrapper around the integrators provided by OpenMM and
+have to be attached to the :class:`Settings` when setting up a simulation
+to provide a way of making the thing shake.
+
+.. class:: VerletIntegrator
+
+ Implementation of Verlet dynamics
+
+
+
+.. class:: BrownianIntegrator
+
+ Implementation of Brownian dynamics
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float`
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float`
+
+ .. method:: SetFriction(friction)
+
+ :param friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: :class:`int`
+
+
+
+
+.. class:: LangevinIntegrator
+
+ Implementation of the Langevin dynamics
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float`
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float`
+
+ .. method:: SetFriction(friction)
+
+ :param friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: :class:`int`
+
+
+
+.. class:: VariableVerletIntegrator
+
+ Implementation of Verlet dynamics with variable time steps
+
+ .. method:: GetErrorTolerance()
+
+ :returns: :class:`float`
+
+ .. method:: SetErrorTolerance(tol)
+
+ :param tol: :class:`float`
+
+
+
+.. class:: VariableLangevinIntegrator
+
+ Implementation of Langevin dynamics with variable time steps
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float`
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float`
+
+ .. method:: SetFriction(friction)
+
+ :param friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: :class:`int`
+
+ .. method:: GetErrorTolerance()
+
+ :returns: :class:`float`
+
+ .. method:: SetErrorTolerance()
+
+ :param tol: :class:`float`
diff --git a/modules/mol/mm/doc/settings.rst b/modules/mol/mm/doc/settings.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a26062ecf448d5cb282ca25c5d470d988c5f7977
--- /dev/null
+++ b/modules/mol/mm/doc/settings.rst
@@ -0,0 +1,253 @@
+The Molecular Mechanis Settings
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The :class:`Settings` define all parameters to control the buildup of a
+:class:`Topology` in the :class:`TopologyCreator` and the final setup
+of the :class:`Simulation` object.
+
+.. class:: Settings
+
+ .. attribute:: add_bonds
+
+ Flag, whether bonds should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_angles
+
+ Flag, whether angles should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_dihedrals
+
+ Flag, whether dihedrals should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_impropers
+
+ Flag, whether impropers should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_cmaps
+
+ Flag, whether cmaps should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_exclusions
+
+ Flag, whether exclusions should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_nonbonded
+
+ Flag, whether nonbonded interactions should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_gbsa
+
+ Flag, whether GBSA interactions should be parametrized
+ in :class:`TopologyCreator`. default: False
+
+ .. attribute:: constrain_hbonds
+
+ Flag, whether bonds involving hydrogens should be constraint
+ in :class:`TopologyCreator`. default: False
+
+ .. attribute:: constrain_bonds
+
+ Flag, whether all bonds should be constraint in
+ :class:`TopologyCreator`. default: False
+
+ .. attribute:: rigid_water
+
+ Flag, whether water molecules should be made rigid in
+ :class:`TopologyCreator`. This is achieved by adding
+ a distance constraint on the the O-H bonds and an additional
+ one between the two hydrogens. default: False
+
+ .. attribute:: strict_interactions
+
+ Makes sure, that an error is thrown when a particular interaction cannot
+ be parametrized with the given forcefield in the :class:`TopologyCreator`.
+ By setting it to False, these cases get just ignored. default: True
+
+ .. attribute:: ideal_bond_length_constraints
+
+ Flag, whether the ideal bond length from the :class:`Forcefield` should be
+ taken for distance constraints in the :class:`TopologyCreator`.
+ :class:`Forcefield` should be taken. The actual distances from the
+ :class:`EntityHandle` get taken otherwise. default: True
+
+ .. attribute:: fix_heavy_atoms
+
+ Flag, whether all heavy atom positions (non hydrogens) should be fixed in
+ space in the :class:`TopologyCreator`. default: False
+
+ .. attribute:: kill_electrostatics
+
+ Flag, whether all charges should just be set to zero in the
+ :class:`TopologyCreator`. default: False
+
+ .. attribute:: generate_disulfid_bonds
+
+ Flag, whether disulfid bonds based on a simple geometric criterion
+ (SG-SG dist < 2.5A) should be built in :class:`TopologyCreator`.
+ default: True
+
+ .. attribute:: nonbonded_method
+
+ Nonbonded method set up at the creation of the :class:`Simulation`.
+ must be one of mm.NoCutoff, mm.CutoffNonPeriodic, mm.CutoffPeriodic
+ mm.Ewald or mm.PME. default: mm.NoCutoff
+
+ .. attribute:: nonbonded_cutoff
+
+ Nonbonded cutoff set when simulation is set up. default: 10.0
+
+ .. attribute:: remove_cmm_motion
+
+ Whether a center of mass remover object should be attached to the
+ :class:`Simulation`. default: True
+
+ .. attribute:: cmm_frequency
+
+ Frequency regarding simulationsteps when the cmm remover should be applied.
+ default: 1
+
+ .. attribute:: periodic_box_extent
+
+ :class:`ost.geom.Vec3` describing the X,Y and Z extents of the rectangular
+ simulation_box defined when setting up the :class:`Simulation`.
+ default: (0,0,0)
+
+ .. attribute:: init_temperature
+
+ Initial simulation velocities get set according to a Boltzman distribution
+ controlled by init_temperature(Kelvin). default: 0.0
+
+ .. attribute:: forcefield
+
+ :class:`Forcefield` that is used in :class:`TopologyCreator`. default: None
+
+ .. attribute:: termini_exceptions
+
+ Use termini other than the defaults set in the :class:`Forcefield` when
+ using :class:`TopologyCreator`. Has to be a :class:`TerminiExceptions`
+ object. default: None
+
+ .. attribute:: platform
+
+ Platform used by OpenMM to do the calculations. Must be one of mm.Reference,
+ mm.CPU, mm.CUDA or mm.OpenCL. If anything else than the reference platform
+ is used, the attribute openmm_plugin_directory has to be set accordingly.
+ default: mm.Reference
+
+ .. attribute:: add_thermostat
+
+ Flag, whether an Andersen thermostat should be attached when settings up
+ the :class:`Simulation`. default: False
+
+ .. attribute:: thermostat_temperature
+
+ Temperature for the Andersen thermostat. default: NaN
+
+ .. attribute:: thermostat_collision_frequency
+
+ Collision frequency of the Andersen thermostat. default: NaN
+
+ .. attribute:: add_barostat
+
+ Flag, whether an MonteCarlo barostat should be attached when settings up
+ the :class:`Simulation`. default: False
+
+ .. attribute:: barostat_temperature
+
+ Temperature for the MonteCarlo Barostat. default: NaN
+
+ .. attribute:: barostat_pressure
+
+ Pressure for the MonteCarlo Barostat. default: NaN
+
+ .. attribute:: barostat_frequency
+
+ Frequency of the MonteCarlo Barostat. default: 25
+
+ .. attribute:: integrator
+
+ Integrator to move the simulation forward in time. OpenMM offers following
+ Integrators: :class:`VerletIntegrator`, :class:`BrownianIntegrator`,
+ :class:`LangevinIntegrator`, :class:`VariableVerletIntegrator` and
+ :class:`VariableLangevinIntegrator`. default: None
+
+ .. attribute:: solvent_dielectric
+
+ Solvent dielectric constant. This is used for the GBSA force when the
+ :class:`Simulation` gets set up. default: 78.3
+
+ .. attribute:: solute_dielectric
+
+ Solute dielectric constant. This is used for the GBSA force when the
+ :class:`Simulation` gets set up. default: 1.0
+
+ .. attribute:: reaction_field_dielecric
+
+ Sets the reaction field dielectric for the Nonbonded Force when setting
+ up the :class:`Simulation`. default: 78.3
+
+ .. attribute:: use_dispersion_correction
+
+ Flag, whether the dispersion correction should be used when setting
+ up the Nonbonded Force in the :class:`Simulation`. default: True
+
+ .. attribute:: keep_ff_specific_naming
+
+ When running through the :class:`TopologyCreator`, the given ent gets
+ renamed to the forcefield specific naming. If set to true, the naming
+ stays like that, if not the entity gets renamed to PDB standard.
+ default: True
+
+ .. attribute:: openmm_plugin_directory
+
+ Path, where OpenMM specific plugins are searched. Especially if you want
+ to use other platforms than reference, this has to be set.
+ default: "/usr/local/openmm/lib/plugins"
+
+ .. attribute:: custom_plugin_directory
+
+ Path, where custom plugins are searched.
+ default: "/usr/local/openmm/lib/plugins"
+
+
+
+
+.. class:: TerminiExceptions
+
+ Can be used to define exceptions from the standard assignments
+ assigned in the :class:`Forcefield`.
+
+ .. method:: SetException(res, exception_name)
+
+ :param res: :class:`ResidueHandle` for which the exception
+ should be set.
+
+ :param exception_name: :class:`str` describing the name of the
+ Blockmodifier in the forcefield that should be
+ applied in case of a termini
+
+ .. method:: HasException(res)
+
+ :param res: :class:`ResidueHandle` that should be checked for
+ exceptions
+
+ :returns: :class:`bool` True if res has an exception
+
+ .. method:: GetException(res)
+
+ :param res: :class:`ResidueHandle` containing the exception
+
+ :raises: :class:`RuntimeError` if res has no associated exception
+
+ :returns: :class:`str` describint the name of the Blockmodifier in
+ the forcefield, that should be applied in case of a
+ termini
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index ef20c0f4704b21b4cdac46472b2de8c60c732b1b..5fb169e76eea21d677883bf831a8fab3993963bb 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -23,8 +23,25 @@ that should suffice most needs.
based on the information given by the :class:`Settings`/:class:`Forcefield`.
:param entity: :class:`EntityHandle`
+
:param settings: :class:`Settings`
+ :raises: :class:`RuntimeError` if settings has no
+ :class:`Forcefield` assigned
+
+ :raises: :class:`RuntimeError` if there is a residue with no
+ appropriate :class:`BuildingBlock` in the
+ :class:`Forcefield`
+
+ :raises: :class:`RuntimeError` if there is a
+ :class:`ResidueHandle` not matching the
+ :class:`BuildingBlock` definition in the
+ :class:`Forcefield`
+
+ :raises: :class:`RuntimeError` if there is an interaction,
+ that has no parameters in the forcefield. This
+ :class:`RuntimeError` can be supressed by the
+ according flag in the :class:`Settings` object.
.. class:: Topology