: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/AmberTools.php>`_
and were converted using the `openmmforcefields <https://github.com/openmm/openmmforcefields>`_ package and `ParmEd <https://github.com/parmed/parmed>`_.
and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
Amber19
-------
Updated protein and DNA force fields from the
`AmberTools 24 release <http://ambermd.org/AmberTools.php>`_ are also available.
.. 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
...
...
@@ -595,8 +614,18 @@ such as :file:`charmm36/water.xml`, which specifies the default CHARMM water mod
`CHARMM-GUI<http://charmm-gui.org/>`_,it's easiest to load
the PSF file directly, as discussed in Section :numref:`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 `openmmforcefields <https://github.com/openmm/openmmforcefields>`_ package and `parmed <https://github.com/parmed/parmed>`_.
.. warning:: Some residues and patches are not included in this port of
CHARMM36, either due to a lack of support for certain CHARMM
features in `ParmEd <https://github.com/parmed/parmed>`_, or
because they generate a large number of residue-patch combinations,
slowing down parameterization. The openmmforcefields_ package
includes residues and patches not present in this port within
additional force field XML files that can be loaded as needed.
The converted parameter sets come from the
`CHARMM36 July 2024 update <http://mackerell.umaryland.edu/charmm_ff.shtml>`_,
which includes the CHARMM36m protein parameters. They were converted using the
openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
Implicit Solvent
----------------
...
...
@@ -681,8 +710,8 @@ recommended for most simulations.
CHARMM Polarizable Force Field
------------------------------
To use the CHARMM 2019 polarizable force field\ :cite:`Lopes2013`, include the
single file :file:`charmm_polar_2019.xml`. It includes parameters for proteins, lipids,
To use the CHARMM 2023 polarizable force field\ :cite:`Lopes2013`, include the
single file :file:`charmm_polar_2023.xml`. It includes parameters for proteins, lipids, carbohydrates,
water, and ions. When using this force field, remember to add extra particles to
the :class:`Topology` as described in section :numref:`adding-or-removing-extra-particles`.
This force field also requires that you use one of the special integrators that
...
...
@@ -698,17 +727,19 @@ still useful for reproducing older results.
title={ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution},
author={Tian, C. and Kasavajhala, K. and Belfon, K.A.A. and Raguette, L. and Huang, H. and Migues, A.N. and Bickel, J. and Wang, Y. and Pincay, J. and Wu, Q. and Simmerling, C.},
journal={Journal of Chemical Theory and Computation},
volume={16},
pages={528-552},
year={2020},
doi={10.1021/acs.jctc.9b00591},
type={Journal Article}
}
@article{Zgarbova2021,
title={Z-DNA as a touchstone for additive empirical force fields and a refinement of the alpha/gamma DNA torsions for AMBER},
author={Zgarbova, M. and Sponer, J. and Jurecka, P.},
journal={Journal of Chemical Theory and Computation},
