.. tip:: The solvent model XML files included under the :file:`amber14/` directory
include both water *and* ions compatible with that water model, so if you
mistakenly specify :file:`tip3p.xml` instead of :file:`amber14/tip3p.xml`,
you run the risk of having :class:`ForceField` throw an exception since
:file:`tip3p.xml` will be missing parameters for ions in your system.
The converted parameter sets come from the `AmberTools 17 release <http://ambermd.org/AmberTools17-get.html>`_
and were converted using the `openmm-forcefields <https://github.com/choderalab/openmm-forcefields>`_ package and `ParmEd <https://github.com/parmed/parmed>`_.
CHARMM36
--------
The CHARMM36\ :cite:`Best2012` force field provides parameters for proteins, DNA,
RNA, lipids, carbohydrates, water, ions, and various small molecules.
RNA, lipids, carbohydrates, water, ions, and various small molecules (see `here <http://mackerell.umaryland.edu/charmm_ff.shtml#refs>`_
for full references).
.. tabularcolumns:: |l|L|
...
...
@@ -609,6 +623,52 @@ File Parameters
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
.. warning:: Drude polarizable sites and lone pairs are not yet supported
by `ParmEd <https://github.com/parmed/parmed>`_ and the CHARMM36 forcefields
that depend on these features are not included in this port.
To use the CHARMM 2013 polarizable force field\ :cite:`Lopes2013`,
include the single file :file:`charmm_polar_2013.xml`.
.. tip:: The solvent model XML files included under the :file:`charmm36/` directory
include both water *and* ions compatible with that water model, so if you
mistakenly specify :file:`tip3p.xml` instead of :file:`charmm36/water.xml`,
you run the risk of having :class:`ForceField` raise an exception due to
missing parameters for ions in your system.
.. tip:: CHARMM makes extensive use of patches, which are automatically combined with
residue templates to create an expanded library of patched residue templates
by :class:`ForceField`. That means that patched residues, such as ``ACE`` and
``NME`` patched termini, must occur as a single residue in order for :class:`ForceField`
to correctly match the residue template and apply parameters. Since these
patched residues are not standard PDB residues, :class:`Modeller` does not know
how to add hydrogens to these nonstandard residues, and your input topologies
must already contain appropriate hydrogens. This can often cause problems when
trying to read in PDB files from sources such as `CHARMM-GUI <http://charmm-gui.org/>`_
that do not generate PDB files that comply with the `PDB standard <http://www.wwpdb.org/documentation/file-format>`_.
If you'reusingfilesfrom`CHARMM-GUI<http://charmm-gui.org/>`_,it's easiest to load
the PSF file directly, as discussed in Section :ref:`using-charmm-files`.
.. tip:: Trying to read in PDB files from sources such as `CHARMM-GUI <http://charmm-gui.org/>`_
that do not generate PDB files that comply with the `PDB standard <http://www.wwpdb.org/documentation/file-format>`_
and omit ``CONECT`` records specifying bonds between residues (such as cysteines)
or include ``CONECT`` records specifying non-chemical ``H-H`` bonds in waters
can cause issues with the detection and parameter assignment for disulfide bonds.
Make sure the files you read in comply with the appropriate standards regarding
additional bonds and nonstandard residue definitions. If you'reusingfilesfrom
`CHARMM-GUI<http://charmm-gui.org/>`_,it's easiest to load
the PSF file directly, as discussed in Section :ref:`using-charmm-files`.
The converted parameter sets come from the `CHARMM36 July 2017 update <http://mackerell.umaryland.edu/charmm_ff.shtml>`_
and were converted using the `openmm-forcefields <https://github.com/choderalab/openmm-forcefields>`_ package and `parmed <https://github.com/parmed/parmed>`_.
