.. 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 neglecting critical 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
CHARMM36
--------
--------
The CHARMM36\ :cite:`Best2012` force field provides parameters for proteins, DNA,
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|
.. tabularcolumns:: |l|L|
...
@@ -609,6 +622,44 @@ File Parameters
...
@@ -609,6 +622,44 @@ File Parameters
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
: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 CHARMM36 forcefields that
depend on these features have not yet been converted.
.. 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/tip3p.xml`,
you run the risk of neglecting critical 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>`_.
.. 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.
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>`_.
