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Merge branch 'master' into membrane

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devtools/ci/jenkins/install.sh
View file @ 65920c60
...@@ -11,7 +11,7 @@ cmake --version ...@@ -11,7 +11,7 @@ cmake --version
echo "Using clang (`which clang`) version:" echo "Using clang (`which clang`) version:"
clang --version clang --version
module load cuda conda/jenkins module load cuda/${CUDA_VERSION} conda/jenkins
# Constants # Constants
CONDAENV=openmm-test-3.5 CONDAENV=openmm-test-3.5
...@@ -22,8 +22,11 @@ export OPENMM_CUDA_COMPILER=`which nvcc` ...@@ -22,8 +22,11 @@ export OPENMM_CUDA_COMPILER=`which nvcc`
# Create a conda environment, but clean up after one first. If it doesn't exist, don't complain. # Create a conda environment, but clean up after one first. If it doesn't exist, don't complain.
# But since we are invoking this shell with -e (exit on all errors), we need || true to prevent this # But since we are invoking this shell with -e (exit on all errors), we need || true to prevent this
# command from crashing the whole shell # command from crashing the whole shell
create_conda_env() {
conda create -yn ${CONDAENV} python=3.5 --no-default-packages --quiet
}
conda remove -yn ${CONDAENV} --all --quiet || true conda remove -yn ${CONDAENV} --all --quiet || true
conda create -yn ${CONDAENV} python=3.5 --no-default-packages --quiet create_conda_env || create_conda_env # Crappy way to work around conda concurrency restrictions
conda install -yn ${CONDAENV} numpy scipy pytest --quiet conda install -yn ${CONDAENV} numpy scipy pytest --quiet
source activate ${CONDAENV} # enter our new environment source activate ${CONDAENV} # enter our new environment
...@@ -40,4 +43,4 @@ python devtools/run-ctest.py --job-duration=120 --timeout 300 ...@@ -40,4 +43,4 @@ python devtools/run-ctest.py --job-duration=120 --timeout 300
# Now remove the conda environment # Now remove the conda environment
source deactivate source deactivate
conda remove -yn ${CONDAENV} --all --quiet conda remove -yn ${CONDAENV} --all --quiet
\ No newline at end of file
docs-source/usersguide/application.rst
View file @ 65920c60
...@@ -314,7 +314,7 @@ A First Example ...@@ -314,7 +314,7 @@ A First Example
*************** ***************
Let’s begin with our first example of an OpenMM script. It loads a PDB file Let’s begin with our first example of an OpenMM script. It loads a PDB file
called :file:`input.pdb` that defines a biomolecular system, parameterizes it using the Amber99SB force field and TIP3P water called :file:`input.pdb` that defines a biomolecular system, parameterizes it using the Amber14 force field and TIP3P-FB water
model, energy minimizes it, simulates it for 10,000 steps with a Langevin model, energy minimizes it, simulates it for 10,000 steps with a Langevin
integrator, and saves a snapshot frame to a PDB file called :file:`output.pdb` every 1000 time integrator, and saves a snapshot frame to a PDB file called :file:`output.pdb` every 1000 time
steps. steps.
...@@ -328,7 +328,7 @@ steps. ...@@ -328,7 +328,7 @@ steps.
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml') forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=1*nanometer, constraints=HBonds) nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds) integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
...@@ -390,14 +390,14 @@ Make sure you include the single quotes around the file name. OpenMM also can l ...@@ -390,14 +390,14 @@ Make sure you include the single quotes around the file name. OpenMM also can l
files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`. files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`.
:: ::
forcefield = ForceField('amber99sb.xml', 'tip3p.xml') forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
This line specifies the force field to use for the simulation. Force fields are This line specifies the force field to use for the simulation. Force fields are
defined by XML files. OpenMM includes XML files defining lots of standard force fields (see Section :ref:`force-fields`). defined by XML files. OpenMM includes XML files defining lots of standard force fields (see Section :ref:`force-fields`).
If you find you need to extend the repertoire of force fields available, If you find you need to extend the repertoire of force fields available,
you can find more information on how to create these XML files in Chapter :ref:`creating-force-fields`. you can find more information on how to create these XML files in Chapter :ref:`creating-force-fields`.
In this case we load two of those files: :file:`amber99sb.xml`, which contains the In this case we load two of those files: :file:`amber14-all.xml`, which contains the
Amber99SB force field, and :file:`tip3p.xml`, which contains the TIP3P water model. The Amber14 force field, and :file:`amber14/tip3pfb.xml`, which contains the TIP3P-FB water model. The
:class:`ForceField` object is assigned to a variable called :code:`forcefield`\ . :class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
:: ::
...@@ -760,57 +760,124 @@ the main force field, and possibly a second file to define the water model ...@@ -760,57 +760,124 @@ the main force field, and possibly a second file to define the water model
(either implicit or explicit). For example: (either implicit or explicit). For example:
:: ::
forcefield = ForceField('amber99sb.xml', 'tip3p.xml') forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
In some cases, one XML file may load several others. For example, :file:`amber14-all.xml`
is really just a shortcut for loading several different files that together make up
the AMBER14 force field. If you need finer grained control over which parameters
are loaded, you can instead specify the component files individually.
Be aware that some force fields and water models include "extra particles", such
as lone pairs or Drude particles. Examples include the CHARMM polarizable force
field and all of the 4 and 5 site water models. To use these force fields, you
must first add the extra particles to the :class:`Topology`. See section
:ref:`adding-or-removing-extra-particles` for details.
For the main force field, OpenMM provides the following options: Amber14
-------
The Amber14\ :cite:`Maier2015` force field is made up of various files that define
parameters for proteins, DNA, RNA, lipids, water, and ions.
.. tabularcolumns:: |l|L|
=================================== ============================================
File Parameters
=================================== ============================================
:file:`amber14/protein.ff14SB.xml` Protein (recommended)
:file:`amber14/protein.ff15ipq.xml` Protein (alternative)
:file:`amber14/DNA.OL15.xml` DNA (recommended)
:file:`amber14/DNA.bsc1.xml` DNA (alternative)
:file:`amber14/RNA.OL3.xml` RNA
:file:`amber14/lipid17.xml` Lipid
:file:`amber14/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions
:file:`amber14/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
=================================== ============================================
As a convenience, the file :file:`amber14-all.xml` can be used as a shortcut to include
:file:`amber14/protein.ff14SB.xml`, :file:`amber14/DNA.OL15.xml`, :file:`amber14/RNA.OL3.xml`,
and :file:`amber14/lipid17.xml`. In most cases you can simply include that file,
plus one of the water models.
CHARMM36
--------
The CHARMM36\ :cite:`Best2012` force field provides parameters for proteins, DNA,
RNA, lipids, carbohydrates, water, ions, and various small molecules.
.. tabularcolumns:: |l|L|
================================= ============================================
File Parameters
================================= ============================================
:file:`charmm36.xml` Protein, DNA, RNA, lipids, carbohydrates, and small molecules
:file:`charmm36/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions
:file:`charmm36/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:file:`charmm36/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions
:file:`charmm36/tip3p-pme-f.xml` TIP3P-PME-F water model\ :cite:`Price2004` and ions
:file:`charmm36/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`charmm36/tip4p2005.xml` TIP4P-2005 water model\ :cite:`Abascal2005` and ions
:file:`charmm36/tip5p.xml` TIP5P water model\ :cite:`Mahoney2000` and ions
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
================================= ============================================
AMOEBA
------
The AMOEBA polarizable force field provides parameters for proteins, water, and ions.
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
============================= ================================================================================ ============================= ================================================================================
File Force Field File Parameters
============================= ================================================================================ ============================= ================================================================================
:code:`amber96.xml` Amber96\ :cite:`Kollman1997` :file:`amoeba2013.xml` AMOEBA 2013\ :cite:`Shi2013`
:code:`amber99sb.xml` Amber99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006` :file:`amoeba2013_gk.xml` Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2013 force field
:code:`amber99sbildn.xml` Amber99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010` :file:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
:code:`amber99sbnmr.xml` Amber99SB with modifications to fit NMR data\ :cite:`Li2010`
:code:`amber03.xml` Amber03\ :cite:`Duan2003`
:code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`)
:code:`amberfb15.xml` AMBER-FB15\ :cite:`Wang2017`. Intramolecular parameters optimized with
ForceBalance using high-level ab initio data.
:code:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead. recommended to use AMOEBA 2013 instead.
:code:`amoeba2013.xml` AMOEBA 2013\ :cite:`Shi2013` :file:`amoeba2009_gk.xml` Generalized Kirkwood solvation model for use with AMOEBA 2009 force field
:code:`charmm_polar_2013.xml` CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
============================= ================================================================================ ============================= ================================================================================
For explicit solvent simulations, just include the single file :file:`amoeba2013.xml`.
AMOEBA also supports implicit solvent using a Generalized Kirkwood model. To enable
it, also include :file:`amoeba2013_gk.xml`.
The AMBER files do not include parameters for water molecules. This allows you The older AMOEBA 2009 force field is provided only for backward compatibility, and is not
to separately select which water model you want to use. For simulations that recommended for most simulations.
include explicit water molecules, you should also specify one of the following
files:
.. tabularcolumns:: |l|L| CHARMM Polarizable Force Field
------------------------------
=================== ============================================ To use the CHARMM 2013 polarizable force field\ :cite:`Lopes2013`, include the
File Water Model single file :file:`charmm_polar_2013.xml`. It includes parameters for proteins,
=================== ============================================ water, and ions. When using this force field, remember to add extra particles to
:code:`tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` the :class:`Topology` as described in section :ref:`adding-or-removing-extra-particles`.
:code:`tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014`
:code:`tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` Older Amber Force Fields
:code:`tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` ------------------------
:code:`tip5p.xml` TIP5P water model\ :cite:`Mahoney2000`
:code:`spce.xml` SPC/E water model\ :cite:`Berendsen1987`
:code:`swm4ndp.xml` SWM4-NDP water model\ :cite:`Lamoureux2006`
=================== ============================================
OpenMM includes several older Amber force fields as well. For most simulations
Amber14 is preferred over any of these, but they are still useful for reproducing
older results.
For the polarizable force fields (AMOEBA and CHARMM), only one explicit water model .. tabularcolumns:: |l|L|
is currently available and the water parameters are included in the same file as
the macromolecule parameters. Also, the polarizable force fields only include
parameters for amino acids and ions, not for nucleic acids.
If you want to include an implicit solvation model, you can also specify one of ============================= ================================================================================
the following files: File Force Field
============================= ================================================================================
:code:`amber96.xml` Amber96\ :cite:`Kollman1997`
:code:`amber99sb.xml` Amber99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
:code:`amber99sbildn.xml` Amber99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
:code:`amber99sbnmr.xml` Amber99SB with modifications to fit NMR data\ :cite:`Li2010`
:code:`amber03.xml` Amber03\ :cite:`Duan2003`
:code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`)
============================= ================================================================================
Several of these force fields support implicit solvent. To enable it, also
include the corresponding OBC file.
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
...@@ -818,37 +885,37 @@ the following files: ...@@ -818,37 +885,37 @@ the following files:
File Implicit Solvation Model File Implicit Solvation Model
========================= ================================================================================================= ========================= =================================================================================================
:code:`amber96_obc.xml` GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with Amber96 force field :code:`amber96_obc.xml` GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with Amber96 force field
:code:`amber99_obc.xml` GBSA-OBC solvation model for use with Amber99 force fields :code:`amber99_obc.xml` GBSA-OBC solvation model for use with Amber99 force field and its variants
:code:`amber03_obc.xml` GBSA-OBC solvation model for use with Amber03 force field :code:`amber03_obc.xml` GBSA-OBC solvation model for use with Amber03 force field
:code:`amber10_obc.xml` GBSA-OBC solvation model for use with Amber10 force field :code:`amber10_obc.xml` GBSA-OBC solvation model for use with Amber10 force field
:code:`amoeba2009_gk.xml` Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
:code:`amoeba2013_gk.xml` Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
========================= ================================================================================================= ========================= =================================================================================================
For example, to use the GBSA-OBC solvation model with the Amber99SB force field,
you would type:
::
forcefield = ForceField('amber99sb.xml', 'amber99_obc.xml')
Note that the GBSA-OBC parameters in these files are those used in TINKER.\ :cite:`Tinker` Note that the GBSA-OBC parameters in these files are those used in TINKER.\ :cite:`Tinker`
They are designed for use with Amber force fields, but they are different from They are designed for use with Amber force fields, but they are different from
the parameters found in the AMBER application. the parameters found in the AMBER application.
If you are running a vacuum simulation, you do not need to specify a water Water Models
model. The following line specifies the Amber10 force field and no water model. ------------
If you try to use it with a PDB file that contains explicit water, it will
produce an error since no water parameters are defined:
::
forcefield = ForceField('amber10.xml') The following files define popular water models. They can be used with force fields
that do not provide their own water models. When using Amber14 or CHARMM36, use
the water files included with those force fields instead, since they also include
ion parameters.
.. tabularcolumns:: |l|L|
=================== ============================================
File Water Model
=================== ============================================
:code:`tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983`
:code:`tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014`
:code:`tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004`
:code:`tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014`
:code:`tip5p.xml` TIP5P water model\ :cite:`Mahoney2000`
:code:`spce.xml` SPC/E water model\ :cite:`Berendsen1987`
:code:`swm4ndp.xml` SWM4-NDP water model\ :cite:`Lamoureux2006`
=================== ============================================
Be aware that some force fields and water models include "extra particles", such
as lone pairs or Drude particles. Examples include the CHARMM polarizable force
field and all of the 4 and 5 site water models. To use these force fields, you
must first add the extra particles to the :class:`Topology`. See section
:ref:`adding-or-removing-extra-particles` for details.
AMBER Implicit Solvent AMBER Implicit Solvent
====================== ======================
...@@ -2959,12 +3026,6 @@ relative either to the directory containing the parent XML file (the one with ...@@ -2959,12 +3026,6 @@ relative either to the directory containing the parent XML file (the one with
the :code:`<Include>` tag) or the OpenMM data directory (the one containing the :code:`<Include>` tag) or the OpenMM data directory (the one containing
built in force fields). built in force fields).
The included file is fully processed before any other tags in the parent file
are processed, and its definitions are added to the force field. This means the
parent file can refer to atom types defined in the included file, but not the
other way around. If there are multiple :code:`<Include>` tags, they are processed
in the order they appear in the file.
Using Multiple Files Using Multiple Files
******************** ********************
......
docs-source/usersguide/references.bib
View file @ 65920c60
@article{Abascal2005
author = {Abascal, J.L.F. and Vega, C.},
title = {A general purpose model for the condensed phases of water: TIP4P/2005},
journal = {Journal of Chemical Physics},
volume = {123},
pages = {234505},
year = {2005},
type = {Journal Article}
}
@article{Andersen1980 @article{Andersen1980
author = {Andersen, Hans C.}, author = {Andersen, Hans C.},
title = {Molecular dynamics simulations at constant pressure and/or temperature}, title = {Molecular dynamics simulations at constant pressure and/or temperature},
...@@ -29,6 +39,17 @@ ...@@ -29,6 +39,17 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Best2012,
author = {Best, Robert B. and Zhu, Xiao and Shim, Jihyun and Lopes, Pedro E. M. and Mittal, Jeetain and Feig, Michael and MacKerell, Alexander D.},
title = {Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles},
journal = {Journal of Chemical Theory and Computation},
volume = {8},
number = {9},
pages = {3257-3273},
year = {2012},
type = {Journal Article}
}
@article{Ceriotti2010 @article{Ceriotti2010
author = {Ceriotti, M. and Parrinello, M. and Markland, Thomas E. and Manolopoulos, David E.}, author = {Ceriotti, M. and Parrinello, M. and Markland, Thomas E. and Manolopoulos, David E.},
title = {Efficient stochastic thermostatting of path integral molecular dynamics}, title = {Efficient stochastic thermostatting of path integral molecular dynamics},
...@@ -258,6 +279,17 @@ ...@@ -258,6 +279,17 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Maier2015
author = {Maier, James A. and Martinez, Carmenza and Kasavajhala, Koushik and Wickstrom, Lauren and Hauser, Kevin E. and Simmerling, Carlos},
title = {ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {8},
pages = {3696-3713},
year = {2015},
type = {Journal Article}
}
@article{Markland2008 @article{Markland2008
author = {Markland, Thomas E. and Manolopoulos, David E.}, author = {Markland, Thomas E. and Manolopoulos, David E.},
title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations}, title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
...@@ -318,6 +350,16 @@ ...@@ -318,6 +350,16 @@
type = {Personal Communication} type = {Personal Communication}
} }
@article{Price2004
author = {Price, D.J. and Brooks, C.L. III},
title = {A modified TIP3P water potential for simulation with Ewald summation},
journal = {Journal of Chemical Physics},
volume = {121},
pages = {10096-10103},
year = {2004},
type = {Journal Article}
}
@article{Ren2002 @article{Ren2002
author = {Ren, P. and Ponder, Jay W.}, author = {Ren, P. and Ponder, Jay W.},
title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations}, title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
...@@ -338,6 +380,16 @@ ...@@ -338,6 +380,16 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Rick2004
author = {Rick, S.W.},
title = {A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums},
journal = {Journal of Chemical Physics},
volume = {120},
pages = {6085-6093},
year = {2004},
type = {Journal Article}
}
@article{Schaefer1998 @article{Schaefer1998
author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin}, author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model}, title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
......
examples/simulatePdb.py
View file @ 65920c60
...@@ -4,7 +4,7 @@ from simtk.unit import * ...@@ -4,7 +4,7 @@ from simtk.unit import *
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml') forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds) system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds) integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(pdb.topology, system, integrator) simulation = Simulation(pdb.topology, system, integrator)
......
wrappers/python/setup.py
View file @ 65920c60
...@@ -146,7 +146,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM, ...@@ -146,7 +146,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
setupKeywords["package_data"] = {"simtk" : [], setupKeywords["package_data"] = {"simtk" : [],
"simtk.unit" : [], "simtk.unit" : [],
"simtk.openmm" : [], "simtk.openmm" : [],
"simtk.openmm.app" : ['data/*.xml', 'data/*.pdb'], "simtk.openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/charmm36/*.xml'],
"simtk.openmm.app.internal" : []} "simtk.openmm.app.internal" : []}
setupKeywords["platforms"] = ["Linux", "Mac OS X", "Windows"] setupKeywords["platforms"] = ["Linux", "Mac OS X", "Windows"]
setupKeywords["description"] = \ setupKeywords["description"] = \
......
wrappers/python/simtk/openmm/app/data/amber14-all.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Include file="amber14/protein.ff14SB.xml"/>
<Include file="amber14/DNA.OL15.xml"/>
<Include file="amber14/RNA.OL3.xml"/>
<Include file="amber14/lipid17.xml"/>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/amber14/DNA.OL15.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="leaprc.DNA.OL15" md5hash="6533cbdef9b6113f090d5cb24752db33" sourcePackage="AmberTools" sourcePackageVersion="17">leaprc.DNA.OL15</Source>
<Reference>Zgarbova, M.; Sponer, J.; Otyepka, M.; Cheatham, T.E. III; Galindo-Murillo, R.; Jurecka, P. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. J. Chem. Theor. and Comp., 2015, 12, 5723-5736.</Reference>
</Info>
<AtomTypes>
<Type class="C" element="C" mass="12.01" name="DNA-C"/>
<Type class="CA" element="C" mass="12.01" name="DNA-CA"/>
<Type class="CB" element="C" mass="12.01" name="DNA-CB"/>
<Type class="CK" element="C" mass="12.01" name="DNA-CK"/>
<Type class="CM" element="C" mass="12.01" name="DNA-CM"/>
<Type class="CQ" element="C" mass="12.01" name="DNA-CQ"/>
<Type class="CT" element="C" mass="12.01" name="DNA-CT"/>
<Type class="H" element="H" mass="1.008" name="DNA-H"/>
<Type class="HC" element="H" mass="1.008" name="DNA-HC"/>
<Type class="H1" element="H" mass="1.008" name="DNA-H1"/>
<Type class="H2" element="H" mass="1.008" name="DNA-H2"/>
<Type class="HA" element="H" mass="1.008" name="DNA-HA"/>
<Type class="H4" element="H" mass="1.008" name="DNA-H4"/>
<Type class="H5" element="H" mass="1.008" name="DNA-H5"/>
<Type class="HO" element="H" mass="1.008" name="DNA-HO"/>
<Type class="NA" element="N" mass="14.01" name="DNA-NA"/>
<Type class="NB" element="N" mass="14.01" name="DNA-NB"/>
<Type class="NC" element="N" mass="14.01" name="DNA-NC"/>
<Type class="N2" element="N" mass="14.01" name="DNA-N2"/>
<Type class="N*" element="N" mass="14.01" name="DNA-N*"/>
<Type class="O" element="O" mass="16.0" name="DNA-O"/>
<Type class="O2" element="O" mass="16.0" name="DNA-O2"/>
<Type class="OH" element="O" mass="16.0" name="DNA-OH"/>
<Type class="OS" element="O" mass="16.0" name="DNA-OS"/>
<Type class="P" element="P" mass="30.97" name="DNA-P"/>
<Type class="C7" element="C" mass="12.01" name="DNA-C7"/>
<Type class="C2" element="C" mass="12.01" name="DNA-C2"/>
<Type class="C1" element="C" mass="12.01" name="DNA-C1"/>
<Type class="CJ" element="C" mass="12.01" name="DNA-CJ"/>
</AtomTypes>
<Residues>
<Residue name="DA">
<Atom charge="1.1659" name="P" type="DNA-P"/>
<Atom charge="-0.7761" name="OP1" type="DNA-O2"/>
<Atom charge="-0.7761" name="OP2" type="DNA-O2"/>
<Atom charge="-0.4954" name="O5'" type="DNA-OS"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CJ"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
<Atom charge="0.1607" name="C8" type="DNA-C2"/>
<Atom charge="0.1877" name="H8" type="DNA-H5"/>
<Atom charge="-0.6175" name="N7" type="DNA-NB"/>
<Atom charge="0.0725" name="C5" type="DNA-CB"/>
<Atom charge="0.6897" name="C6" type="DNA-CA"/>
<Atom charge="-0.9123" name="N6" type="DNA-N2"/>
<Atom charge="0.4167" name="H61" type="DNA-H"/>
<Atom charge="0.4167" name="H62" type="DNA-H"/>
<Atom charge="-0.7624" name="N1" type="DNA-NC"/>
<Atom charge="0.5716" name="C2" type="DNA-CQ"/>
<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
<Atom charge="0.0713" name="C3'" type="DNA-C7"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.5232" name="O3'" type="DNA-OS"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DA3">
<Atom charge="1.1659" name="P" type="DNA-P"/>
<Atom charge="-0.7761" name="OP1" type="DNA-O2"/>
<Atom charge="-0.7761" name="OP2" type="DNA-O2"/>
<Atom charge="-0.4954" name="O5'" type="DNA-OS"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CJ"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
<Atom charge="0.1607" name="C8" type="DNA-C2"/>
<Atom charge="0.1877" name="H8" type="DNA-H5"/>
<Atom charge="-0.6175" name="N7" type="DNA-NB"/>
<Atom charge="0.0725" name="C5" type="DNA-CB"/>
<Atom charge="0.6897" name="C6" type="DNA-CA"/>
<Atom charge="-0.9123" name="N6" type="DNA-N2"/>
<Atom charge="0.4167" name="H61" type="DNA-H"/>
<Atom charge="0.4167" name="H62" type="DNA-H"/>
<Atom charge="-0.7624" name="N1" type="DNA-NC"/>
<Atom charge="0.5716" name="C2" type="DNA-CQ"/>
<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
<Atom charge="0.0713" name="C3'" type="DNA-C7"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.6549" name="O3'" type="DNA-OH"/>
<Atom charge="0.4396" name="HO3'" type="DNA-HO"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DA5">
<Atom charge="0.4422" name="HO5'" type="DNA-HO"/>
<Atom charge="-0.6318" name="O5'" type="DNA-OH"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CJ"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
<Atom charge="0.1607" name="C8" type="DNA-C2"/>
<Atom charge="0.1877" name="H8" type="DNA-H5"/>
<Atom charge="-0.6175" name="N7" type="DNA-NB"/>
<Atom charge="0.0725" name="C5" type="DNA-CB"/>
<Atom charge="0.6897" name="C6" type="DNA-CA"/>
<Atom charge="-0.9123" name="N6" type="DNA-N2"/>
<Atom charge="0.4167" name="H61" type="DNA-H"/>
<Atom charge="0.4167" name="H62" type="DNA-H"/>
<Atom charge="-0.7624" name="N1" type="DNA-NC"/>
<Atom charge="0.5716" name="C2" type="DNA-CQ"/>
<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
<Atom charge="0.0713" name="C3'" type="DNA-C7"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.5232" name="O3'" type="DNA-OS"/>
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<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DAN">
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<Atom charge="-0.6318" name="O5'" type="DNA-OH"/>
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<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
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<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
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<Atom charge="0.1877" name="H8" type="DNA-H5"/>
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<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
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<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.6549" name="O3'" type="DNA-OH"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
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<Bond atomName1="C8" atomName2="H8"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
</Residue>
<Residue name="DC">
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<Atom charge="0.4314" name="H42" type="DNA-H"/>
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<Atom charge="0.7959" name="C2" type="DNA-C"/>
<Atom charge="-0.6548" name="O2" type="DNA-O"/>
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<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
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<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.5232" name="O3'" type="DNA-OS"/>
<Bond atomName1="P" atomName2="OP1"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
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<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N1"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C6" atomName2="H6"/>
<Bond atomName1="C6" atomName2="C5"/>
<Bond atomName1="C5" atomName2="H5"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C4" atomName2="N4"/>
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<Bond atomName1="N4" atomName2="H41"/>
<Bond atomName1="N4" atomName2="H42"/>
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<Bond atomName1="C2" atomName2="O2"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DC3">
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<Atom charge="-0.7761" name="OP2" type="DNA-O2"/>
<Atom charge="-0.4954" name="O5'" type="DNA-OS"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CJ"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="-0.0116" name="C1'" type="DNA-CT"/>
<Atom charge="0.1963" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0339" name="N1" type="DNA-N*"/>
<Atom charge="-0.0183" name="C6" type="DNA-C1"/>
<Atom charge="0.2293" name="H6" type="DNA-H4"/>
<Atom charge="-0.5222" name="C5" type="DNA-C1"/>
<Atom charge="0.1863" name="H5" type="DNA-HA"/>
<Atom charge="0.8439" name="C4" type="DNA-CA"/>
<Atom charge="-0.9773" name="N4" type="DNA-N2"/>
<Atom charge="0.4314" name="H41" type="DNA-H"/>
<Atom charge="0.4314" name="H42" type="DNA-H"/>
<Atom charge="-0.7748" name="N3" type="DNA-NC"/>
<Atom charge="0.7959" name="C2" type="DNA-C"/>
<Atom charge="-0.6548" name="O2" type="DNA-O"/>
<Atom charge="0.0713" name="C3'" type="DNA-C7"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.6549" name="O3'" type="DNA-OH"/>
<Atom charge="0.4396" name="HO3'" type="DNA-HO"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N1"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C6" atomName2="H6"/>
<Bond atomName1="C6" atomName2="C5"/>
<Bond atomName1="C5" atomName2="H5"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C4" atomName2="N4"/>
<Bond atomName1="C4" atomName2="N3"/>
<Bond atomName1="N4" atomName2="H41"/>
<Bond atomName1="N4" atomName2="H42"/>
<Bond atomName1="N3" atomName2="C2"/>
<Bond atomName1="C2" atomName2="O2"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DC5">
<Atom charge="0.4422" name="HO5'" type="DNA-HO"/>
<Atom charge="-0.6318" name="O5'" type="DNA-OH"/>
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<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
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<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="-0.0116" name="C1'" type="DNA-CT"/>
<Atom charge="0.1963" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0339" name="N1" type="DNA-N*"/>
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<Atom charge="0.2293" name="H6" type="DNA-H4"/>
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<Atom charge="0.1863" name="H5" type="DNA-HA"/>
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<Atom charge="-0.7748" name="N3" type="DNA-NC"/>
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<Atom charge="-0.6548" name="O2" type="DNA-O"/>
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<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
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<Bond atomName1="C5" atomName2="H5"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DCN">
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<Atom charge="-0.7748" name="N3" type="DNA-NC"/>
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<Bond atomName1="N1" atomName2="C6"/>
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</Residue>
<Residue name="DG">
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</Residue>
<Residue name="DG3">
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<ExternalBond atomName="P"/>
</Residue>
<Residue name="DG5">
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<Bond atomName1="N2" atomName2="H22"/>
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<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DGN">
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<Atom charge="0.7432" name="C2" type="DNA-CA"/>
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<Atom charge="0.4235" name="H22" type="DNA-H"/>
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<Proper k1="0.0" periodicity1="3" phase1="0.0" type1="" type2="DNA-C1" type3="DNA-CT" type4=""/>
<Proper k1="7.740400000000001" periodicity1="2" phase1="3.141592653589793" type1="" type2="DNA-C1" type3="DNA-N*" type4=""/>
<Proper k1="1.58992" k2="4.811599999999999" periodicity1="3" periodicity2="1" phase1="3.141592653589793" phase2="0.0" type1="DNA-HC" type2="DNA-CT" type3="DNA-C1" type4="DNA-C1"/>
<Proper k1="9.1002" k2="1.2552" periodicity1="2" periodicity2="3" phase1="3.141592653589793" phase2="0.0" type1="DNA-C1" type2="DNA-C1" type3="DNA-C" type4="DNA-O"/>
<Proper k1="6.464238160000001" k2="7.65102976" k3="2.40094656" periodicity1="1" periodicity2="2" periodicity3="3" phase1="0.7084692859572943" phase2="6.2225054450755" phase3="3.1242318635202055" type1="DNA-OS" type2="DNA-CT" type3="DNA-N*" type4="DNA-C2"/>
<Proper k1="2.87662552" k2="8.955726480000001" k3="5.04665712" k4="1.08775632" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="1.9428568900887877" phase2="6.2880757197436745" phase3="2.978233326261628" phase4="1.643880243892907" type1="DNA-OS" type2="DNA-CT" type3="DNA-N*" type4="DNA-C1"/>
<Proper k1="1.6038666666666666" periodicity1="3" phase1="0.0" type1="" type2="DNA-CJ" type3="DNA-OS" type4=""/>
<Proper k1="0.6973333333333334" periodicity1="3" phase1="0.0" type1="" type2="DNA-CJ" type3="DNA-OH" type4=""/>
<Proper k1="0.6508444444444444" periodicity1="3" phase1="0.0" type1="" type2="DNA-CJ" type3="DNA-CT" type4=""/>
<Proper k1="1.6024720000000001" k2="0.41840000000000005" periodicity1="3" periodicity2="2" phase1="0.0" phase2="3.141592653589793" type1="DNA-CT" type2="DNA-OS" type3="DNA-CT" type4="DNA-CJ"/>
<Proper k1="1.046" periodicity1="1" phase1="0.0" type1="DNA-H1" type2="DNA-CJ" type3="DNA-CT" type4="DNA-OS"/>
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<Proper k1="1.046" periodicity1="1" phase1="0.0" type1="DNA-H1" type2="DNA-CT" type3="DNA-CJ" type4="DNA-OH"/>
<Proper k1="0.75312" k2="1.046" k3="0.8368000000000001" periodicity1="3" periodicity2="2" periodicity3="1" phase1="0.0" phase2="3.141592653589793" phase3="3.141592653589793" type1="DNA-CJ" type2="DNA-CT" type3="DNA-CT" type4="DNA-CT"/>
<Proper k1="0.7747973040000001" k2="5.257325704" k3="1.484725872" periodicity1="1" periodicity2="2" periodicity3="3" phase1="0.5549288319349986" phase2="6.142853854002235" phase3="6.235144770452592" type1="DNA-OS" type2="DNA-P" type3="DNA-OS" type4="DNA-CJ"/>
<Proper k1="0.7747973040000001" k2="5.257325704" k3="1.484725872" periodicity1="1" periodicity2="2" periodicity3="3" phase1="0.5549288319349986" phase2="6.142853854002235" phase3="6.235144770452592" type1="DNA-OH" type2="DNA-P" type3="DNA-OS" type4="DNA-CJ"/>
<Proper k1="4.92891936" k2="0.385354768" k3="4.02848072" periodicity1="1" periodicity2="2" periodicity3="3" phase1="3.3331692425337263" phase2="5.159765562356967" phase3="6.0754099683820435" type1="DNA-CT" type2="DNA-CT" type3="DNA-CJ" type4="DNA-OS"/>
<Proper k1="4.92891936" k2="0.385354768" k3="4.02848072" periodicity1="1" periodicity2="2" periodicity3="3" phase1="3.3331692425337263" phase2="5.159765562356967" phase3="6.0754099683820435" type1="DNA-CT" type2="DNA-CT" type3="DNA-CJ" type4="DNA-OH"/>
<Proper k1="2.2089428000000004" k2="0.381890416" k3="2.24067844" k4="0.33371584" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.4115165235620262" phase2="3.9033934419015024" phase3="3.1696404437351924" phase4="3.755617461332694" type1="DNA-CT" type2="DNA-CJ" type3="DNA-OS" type4="DNA-P"/>
<Improper k1="43.932" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="" type3="" type4="DNA-O"/>
<Improper k1="43.932" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="" type3="DNA-O2" type4="DNA-O2"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-N2" type2="" type3="" type4="DNA-H"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-NA" type2="" type3="" type4="DNA-H"/>
<Improper k1="43.932" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="" type3="DNA-N2" type4="DNA-N2"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="" type3="" type4="DNA-HA"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CQ" type2="" type3="" type4="DNA-H5"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CK" type2="" type3="" type4="DNA-H5"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CM" type2="" type3="" type4="DNA-H4"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CM" type2="" type3="" type4="DNA-HA"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="" type3="" type4="DNA-H4"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="" type3="" type4="DNA-H5"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-N*" type2="DNA-CB" type3="DNA-CK" type4="DNA-CT"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-N*" type2="DNA-C" type3="DNA-CM" type4="DNA-CT"/>
<Improper k1="43.932" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="DNA-CT" type3="DNA-O" type4="DNA-OH"/>
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CM" type2="DNA-C" type3="DNA-CM" type4="DNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="DNA-CM" type3="DNA-N2" type4="DNA-NC"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="DNA-CB" type3="DNA-N2" type4="DNA-NC"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="DNA-N2" type3="DNA-NA" type4="DNA-NC"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="DNA-CA" type3="DNA-CA" type4="DNA-OH"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="DNA-CA" type3="DNA-CA" type4="DNA-OH"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="DNA-H5" type3="DNA-O" type4="DNA-OH"/>
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CM" type2="DNA-CM" type3="DNA-CT" type4="DNA-HA"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="DNA-CM" type3="DNA-H4" type4="DNA-O"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C" type2="DNA-CA" type3="DNA-CA" type4="DNA-OS"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C2" type2="" type3="" type4="DNA-H5"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-N*" type2="DNA-C2" type3="DNA-CB" type4="DNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C1" type2="" type3="" type4="DNA-H4"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C1" type2="" type3="" type4="DNA-HA"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="DNA-N*" type2="DNA-C" type3="DNA-C1" type4="DNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-C1" type2="DNA-C" type3="DNA-C1" type4="DNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="DNA-CA" type2="DNA-C1" type3="DNA-N2" type4="DNA-NC"/>
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-C"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-CA"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-CB"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-CK"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-CM"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-CQ"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="DNA-CT"/>
<Atom epsilon="0.06568879999999999" sigma="0.10690784617684071" type="DNA-H"/>
<Atom epsilon="0.06568879999999999" sigma="0.2649532787749369" type="DNA-HC"/>
<Atom epsilon="0.06568879999999999" sigma="0.2471353044121301" type="DNA-H1"/>
<Atom epsilon="0.06568879999999999" sigma="0.22931733004932334" type="DNA-H2"/>
<Atom epsilon="0.06276" sigma="0.25996424595335105" type="DNA-HA"/>
<Atom epsilon="0.06276" sigma="0.2510552587719476" type="DNA-H4"/>
<Atom epsilon="0.06276" sigma="0.24214627159054422" type="DNA-H5"/>
<Atom epsilon="0.0" sigma="1.0" type="DNA-HO"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NA"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NB"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NC"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-N2"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-N*"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="DNA-O"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="DNA-O2"/>
<Atom epsilon="0.8803136" sigma="0.3066473387839048" type="DNA-OH"/>
<Atom epsilon="0.7112800000000001" sigma="0.3000012343465779" type="DNA-OS"/>
<Atom epsilon="0.8368000000000001" sigma="0.37417746161894255" type="DNA-P"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="DNA-C7"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-C2"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-C1"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="DNA-CJ"/>
</NonbondedForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/amber14/DNA.bsc1.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="leaprc.DNA.bsc1" md5hash="8c9b56948dc597f8d8930bb798c3e090" sourcePackage="AmberTools" sourcePackageVersion="17">leaprc.DNA.bsc1</Source>
<Reference>Ivani, I.; Dans, P.D.; Noy, A.; Perez, A.; Faustino, I.; Hopsital, A.; Walther, J.; Andrio, P.; Goni, R.; Balaceanu, A.; Portella, G.; Battistini, F.; GelpA, J.L.; Gonzalez, C.; Vendruscolo, M.; Laughton, C.A.; Harris, S.; Case, D.A.; Orozco, M. Parmbsc1: A refined force field for DNA simulations. Nature Meth., 2016, 13, 55-58.</Reference>
</Info>
<AtomTypes>
<Type class="C" element="C" mass="12.01" name="DNA-C"/>
<Type class="CA" element="C" mass="12.01" name="DNA-CA"/>
<Type class="CB" element="C" mass="12.01" name="DNA-CB"/>
<Type class="CI" element="C" mass="12.01" name="DNA-CI"/>
<Type class="CK" element="C" mass="12.01" name="DNA-CK"/>
<Type class="CM" element="C" mass="12.01" name="DNA-CM"/>
<Type class="CQ" element="C" mass="12.01" name="DNA-CQ"/>
<Type class="CT" element="C" mass="12.01" name="DNA-CT"/>
<Type class="H" element="H" mass="1.008" name="DNA-H"/>
<Type class="HC" element="H" mass="1.008" name="DNA-HC"/>
<Type class="H1" element="H" mass="1.008" name="DNA-H1"/>
<Type class="H2" element="H" mass="1.008" name="DNA-H2"/>
<Type class="HA" element="H" mass="1.008" name="DNA-HA"/>
<Type class="H4" element="H" mass="1.008" name="DNA-H4"/>
<Type class="H5" element="H" mass="1.008" name="DNA-H5"/>
<Type class="HO" element="H" mass="1.008" name="DNA-HO"/>
<Type class="NA" element="N" mass="14.01" name="DNA-NA"/>
<Type class="NB" element="N" mass="14.01" name="DNA-NB"/>
<Type class="NC" element="N" mass="14.01" name="DNA-NC"/>
<Type class="N2" element="N" mass="14.01" name="DNA-N2"/>
<Type class="N*" element="N" mass="14.01" name="DNA-N*"/>
<Type class="O" element="O" mass="16.0" name="DNA-O"/>
<Type class="O2" element="O" mass="16.0" name="DNA-O2"/>
<Type class="OH" element="O" mass="16.0" name="DNA-OH"/>
<Type class="OS" element="O" mass="16.0" name="DNA-OS"/>
<Type class="P" element="P" mass="30.97" name="DNA-P"/>
<Type class="CE" element="C" mass="12.001" name="DNA-CE"/>
<Type class="C1" element="C" mass="12.01" name="DNA-C1"/>
<Type class="C2" element="C" mass="12.01" name="DNA-C2"/>
</AtomTypes>
<Residues>
<Residue name="DA">
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<Atom charge="-0.7761" name="OP1" type="DNA-O2"/>
<Atom charge="-0.7761" name="OP2" type="DNA-O2"/>
<Atom charge="-0.4954" name="O5'" type="DNA-OS"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CI"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
<Atom charge="0.1607" name="C8" type="DNA-C1"/>
<Atom charge="0.1877" name="H8" type="DNA-H5"/>
<Atom charge="-0.6175" name="N7" type="DNA-NB"/>
<Atom charge="0.0725" name="C5" type="DNA-CB"/>
<Atom charge="0.6897" name="C6" type="DNA-CA"/>
<Atom charge="-0.9123" name="N6" type="DNA-N2"/>
<Atom charge="0.4167" name="H61" type="DNA-H"/>
<Atom charge="0.4167" name="H62" type="DNA-H"/>
<Atom charge="-0.7624" name="N1" type="DNA-NC"/>
<Atom charge="0.5716" name="C2" type="DNA-CQ"/>
<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
<Atom charge="0.0713" name="C3'" type="DNA-CE"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.5232" name="O3'" type="DNA-OS"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DA3">
<Atom charge="1.1659" name="P" type="DNA-P"/>
<Atom charge="-0.7761" name="OP1" type="DNA-O2"/>
<Atom charge="-0.7761" name="OP2" type="DNA-O2"/>
<Atom charge="-0.4954" name="O5'" type="DNA-OS"/>
<Atom charge="-0.0069" name="C5'" type="DNA-CI"/>
<Atom charge="0.0754" name="H5'" type="DNA-H1"/>
<Atom charge="0.0754" name="H5''" type="DNA-H1"/>
<Atom charge="0.1629" name="C4'" type="DNA-CT"/>
<Atom charge="0.1176" name="H4'" type="DNA-H1"/>
<Atom charge="-0.3691" name="O4'" type="DNA-OS"/>
<Atom charge="0.0431" name="C1'" type="DNA-CT"/>
<Atom charge="0.1838" name="H1'" type="DNA-H2"/>
<Atom charge="-0.0268" name="N9" type="DNA-N*"/>
<Atom charge="0.1607" name="C8" type="DNA-C1"/>
<Atom charge="0.1877" name="H8" type="DNA-H5"/>
<Atom charge="-0.6175" name="N7" type="DNA-NB"/>
<Atom charge="0.0725" name="C5" type="DNA-CB"/>
<Atom charge="0.6897" name="C6" type="DNA-CA"/>
<Atom charge="-0.9123" name="N6" type="DNA-N2"/>
<Atom charge="0.4167" name="H61" type="DNA-H"/>
<Atom charge="0.4167" name="H62" type="DNA-H"/>
<Atom charge="-0.7624" name="N1" type="DNA-NC"/>
<Atom charge="0.5716" name="C2" type="DNA-CQ"/>
<Atom charge="0.0598" name="H2" type="DNA-H5"/>
<Atom charge="-0.7417" name="N3" type="DNA-NC"/>
<Atom charge="0.38" name="C4" type="DNA-CB"/>
<Atom charge="0.0713" name="C3'" type="DNA-CE"/>
<Atom charge="0.0985" name="H3'" type="DNA-H1"/>
<Atom charge="-0.0854" name="C2'" type="DNA-CT"/>
<Atom charge="0.0718" name="H2'" type="DNA-HC"/>
<Atom charge="0.0718" name="H2''" type="DNA-HC"/>
<Atom charge="-0.6549" name="O3'" type="DNA-OH"/>
<Atom charge="0.4396" name="HO3'" type="DNA-HO"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DA5">
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<Atom charge="-0.6318" name="O5'" type="DNA-OH"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DAN">
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</Residue>
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</Residue>
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</Residue>
<Residue name="DCN">
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<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
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<Bond atomName1="N4" atomName2="H41"/>
<Bond atomName1="N4" atomName2="H42"/>
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</Residue>
<Residue name="DG">
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</Residue>
<Residue name="DG3">
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</Residue>
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<ExternalBond atomName="P"/>
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</Residue>
<Residue name="DT3">
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<Atom epsilon="0.06276" sigma="0.25996424595335105" type="DNA-HA"/>
<Atom epsilon="0.06276" sigma="0.2510552587719476" type="DNA-H4"/>
<Atom epsilon="0.06276" sigma="0.24214627159054422" type="DNA-H5"/>
<Atom epsilon="0.0" sigma="1.0" type="DNA-HO"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NA"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NB"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-NC"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-N2"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="DNA-N*"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="DNA-O"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="DNA-O2"/>
<Atom epsilon="0.8803136" sigma="0.3066473387839048" type="DNA-OH"/>
<Atom epsilon="0.7112800000000001" sigma="0.3000012343465779" type="DNA-OS"/>
<Atom epsilon="0.8368000000000001" sigma="0.37417746161894255" type="DNA-P"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="DNA-CE"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-C1"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="DNA-C2"/>
</NonbondedForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/amber14/RNA.OL3.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="leaprc.RNA.OL3" md5hash="14201dcae910ce5af3ef4fcb1c67405a" sourcePackage="AmberTools" sourcePackageVersion="17">leaprc.RNA.OL3</Source>
<Reference>Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T.E.; Jurecka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011, 7, 2886-2902.</Reference>
</Info>
<AtomTypes>
<Type class="C" element="C" mass="12.01" name="RNA-C"/>
<Type class="CA" element="C" mass="12.01" name="RNA-CA"/>
<Type class="CB" element="C" mass="12.01" name="RNA-CB"/>
<Type class="CI" element="C" mass="12.01" name="RNA-CI"/>
<Type class="CP" element="C" mass="12.01" name="RNA-CP"/>
<Type class="CS" element="C" mass="12.01" name="RNA-CS"/>
<Type class="CQ" element="C" mass="12.01" name="RNA-CQ"/>
<Type class="CT" element="C" mass="12.01" name="RNA-CT"/>
<Type class="C5" element="C" mass="12.01" name="RNA-C5"/>
<Type class="C4" element="C" mass="12.01" name="RNA-C4"/>
<Type class="H" element="H" mass="1.008" name="RNA-H"/>
<Type class="H1" element="H" mass="1.008" name="RNA-H1"/>
<Type class="H2" element="H" mass="1.008" name="RNA-H2"/>
<Type class="HA" element="H" mass="1.008" name="RNA-HA"/>
<Type class="H4" element="H" mass="1.008" name="RNA-H4"/>
<Type class="H5" element="H" mass="1.008" name="RNA-H5"/>
<Type class="HO" element="H" mass="1.008" name="RNA-HO"/>
<Type class="NA" element="N" mass="14.01" name="RNA-NA"/>
<Type class="NB" element="N" mass="14.01" name="RNA-NB"/>
<Type class="NC" element="N" mass="14.01" name="RNA-NC"/>
<Type class="N2" element="N" mass="14.01" name="RNA-N2"/>
<Type class="N*" element="N" mass="14.01" name="RNA-N*"/>
<Type class="O" element="O" mass="16.0" name="RNA-O"/>
<Type class="O2" element="O" mass="16.0" name="RNA-O2"/>
<Type class="OH" element="O" mass="16.0" name="RNA-OH"/>
<Type class="OS" element="O" mass="16.0" name="RNA-OS"/>
<Type class="P" element="P" mass="30.97" name="RNA-P"/>
</AtomTypes>
<Residues>
<Residue name="A">
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<Atom charge="-0.776" name="OP1" type="RNA-O2"/>
<Atom charge="-0.776" name="OP2" type="RNA-O2"/>
<Atom charge="-0.4989" name="O5'" type="RNA-OS"/>
<Atom charge="0.0558" name="C5'" type="RNA-CI"/>
<Atom charge="0.0679" name="H5'" type="RNA-H1"/>
<Atom charge="0.0679" name="H5''" type="RNA-H1"/>
<Atom charge="0.1065" name="C4'" type="RNA-CT"/>
<Atom charge="0.1174" name="H4'" type="RNA-H1"/>
<Atom charge="-0.3548" name="O4'" type="RNA-OS"/>
<Atom charge="0.0394" name="C1'" type="RNA-CT"/>
<Atom charge="0.2007" name="H1'" type="RNA-H2"/>
<Atom charge="-0.0251" name="N9" type="RNA-N*"/>
<Atom charge="0.2006" name="C8" type="RNA-C5"/>
<Atom charge="0.1553" name="H8" type="RNA-H5"/>
<Atom charge="-0.6073" name="N7" type="RNA-NB"/>
<Atom charge="0.0515" name="C5" type="RNA-CB"/>
<Atom charge="0.7009" name="C6" type="RNA-CA"/>
<Atom charge="-0.9019" name="N6" type="RNA-N2"/>
<Atom charge="0.4115" name="H61" type="RNA-H"/>
<Atom charge="0.4115" name="H62" type="RNA-H"/>
<Atom charge="-0.7615" name="N1" type="RNA-NC"/>
<Atom charge="0.5875" name="C2" type="RNA-CQ"/>
<Atom charge="0.0473" name="H2" type="RNA-H5"/>
<Atom charge="-0.6997" name="N3" type="RNA-NC"/>
<Atom charge="0.3053" name="C4" type="RNA-CB"/>
<Atom charge="0.2022" name="C3'" type="RNA-CT"/>
<Atom charge="0.0615" name="H3'" type="RNA-H1"/>
<Atom charge="0.067" name="C2'" type="RNA-CT"/>
<Atom charge="0.0972" name="H2'" type="RNA-H1"/>
<Atom charge="-0.6139" name="O2'" type="RNA-OH"/>
<Atom charge="0.4186" name="HO2'" type="RNA-HO"/>
<Atom charge="-0.5246" name="O3'" type="RNA-OS"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="O2'"/>
<Bond atomName1="O2'" atomName2="HO2'"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="A3">
<Atom charge="1.1662" name="P" type="RNA-P"/>
<Atom charge="-0.776" name="OP1" type="RNA-O2"/>
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<Atom charge="-0.4989" name="O5'" type="RNA-OS"/>
<Atom charge="0.0558" name="C5'" type="RNA-CI"/>
<Atom charge="0.0679" name="H5'" type="RNA-H1"/>
<Atom charge="0.0679" name="H5''" type="RNA-H1"/>
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<Atom charge="0.1174" name="H4'" type="RNA-H1"/>
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<Atom charge="0.2006" name="C8" type="RNA-C5"/>
<Atom charge="0.1553" name="H8" type="RNA-H5"/>
<Atom charge="-0.6073" name="N7" type="RNA-NB"/>
<Atom charge="0.0515" name="C5" type="RNA-CB"/>
<Atom charge="0.7009" name="C6" type="RNA-CA"/>
<Atom charge="-0.9019" name="N6" type="RNA-N2"/>
<Atom charge="0.4115" name="H61" type="RNA-H"/>
<Atom charge="0.4115" name="H62" type="RNA-H"/>
<Atom charge="-0.7615" name="N1" type="RNA-NC"/>
<Atom charge="0.5875" name="C2" type="RNA-CQ"/>
<Atom charge="0.0473" name="H2" type="RNA-H5"/>
<Atom charge="-0.6997" name="N3" type="RNA-NC"/>
<Atom charge="0.3053" name="C4" type="RNA-CB"/>
<Atom charge="0.2022" name="C3'" type="RNA-CT"/>
<Atom charge="0.0615" name="H3'" type="RNA-H1"/>
<Atom charge="0.067" name="C2'" type="RNA-CT"/>
<Atom charge="0.0972" name="H2'" type="RNA-H1"/>
<Atom charge="-0.6139" name="O2'" type="RNA-OH"/>
<Atom charge="0.4186" name="HO2'" type="RNA-HO"/>
<Atom charge="-0.6541" name="O3'" type="RNA-OH"/>
<Atom charge="0.4376" name="HO3'" type="RNA-HO"/>
<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="C5" atomName2="C4"/>
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<Bond atomName1="C2" atomName2="N3"/>
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<ExternalBond atomName="P"/>
</Residue>
<Residue name="A5">
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<Atom charge="0.2006" name="C8" type="RNA-C5"/>
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<Atom charge="-0.6997" name="N3" type="RNA-NC"/>
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</Residue>
<Residue name="AN">
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CA" type2="" type3="" type4="RNA-H5"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="RNA-N*" type2="RNA-CB" type3="RNA-CP" type4="RNA-CT"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="RNA-N*" type2="RNA-C" type3="RNA-CS" type4="RNA-CT"/>
<Improper k1="43.932" periodicity1="2" phase1="3.141592653589793" type1="RNA-C" type2="RNA-CT" type3="RNA-O" type4="RNA-OH"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CA" type2="RNA-CA" type3="RNA-CA" type4="RNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CS" type2="RNA-C" type3="RNA-CS" type4="RNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CA" type2="RNA-CS" type3="RNA-N2" type4="RNA-NC"/>
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C" type2="RNA-CA" type3="RNA-CA" type4="RNA-OH"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CA" type2="RNA-CA" type3="RNA-CA" type4="RNA-OH"/>
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C" type2="RNA-H5" type3="RNA-O" type4="RNA-OS"/>
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<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C5" type2="" type3="" type4="RNA-H5"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="RNA-N*" type2="RNA-C5" type3="RNA-CB" type4="RNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C4" type2="" type3="" type4="RNA-H4"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C4" type2="" type3="" type4="RNA-HA"/>
<Improper k1="4.184" periodicity1="2" phase1="3.141592653589793" type1="RNA-N*" type2="RNA-C" type3="RNA-C4" type4="RNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C4" type2="RNA-C" type3="RNA-C4" type4="RNA-CT"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-CA" type2="RNA-C4" type3="RNA-N2" type4="RNA-NC"/>
<Improper k1="4.6024" periodicity1="2" phase1="3.141592653589793" type1="RNA-C" type2="RNA-CA" type3="RNA-CA" type4="RNA-OS"/>
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-C"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-CA"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-CB"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="RNA-CI"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-CP"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-CS"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-CQ"/>
<Atom epsilon="0.4577296" sigma="0.3399669508423535" type="RNA-CT"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-C5"/>
<Atom epsilon="0.359824" sigma="0.3399669508423535" type="RNA-C4"/>
<Atom epsilon="0.06568879999999999" sigma="0.10690784617684071" type="RNA-H"/>
<Atom epsilon="0.06568879999999999" sigma="0.2471353044121301" type="RNA-H1"/>
<Atom epsilon="0.06568879999999999" sigma="0.22931733004932334" type="RNA-H2"/>
<Atom epsilon="0.06276" sigma="0.25996424595335105" type="RNA-HA"/>
<Atom epsilon="0.06276" sigma="0.2510552587719476" type="RNA-H4"/>
<Atom epsilon="0.06276" sigma="0.24214627159054422" type="RNA-H5"/>
<Atom epsilon="0.0" sigma="1.0" type="RNA-HO"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="RNA-NA"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="RNA-NB"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="RNA-NC"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="RNA-N2"/>
<Atom epsilon="0.7112800000000001" sigma="0.3249998523775958" type="RNA-N*"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="RNA-O"/>
<Atom epsilon="0.87864" sigma="0.2959921901149463" type="RNA-O2"/>
<Atom epsilon="0.8803136" sigma="0.3066473387839048" type="RNA-OH"/>
<Atom epsilon="0.7112800000000001" sigma="0.3000012343465779" type="RNA-OS"/>
<Atom epsilon="0.8368000000000001" sigma="0.37417746161894255" type="RNA-P"/>
</NonbondedForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/amber14/lipid17.xml 0 → 100644
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wrappers/python/simtk/openmm/app/data/amber14/protein.ff14SB.xml 0 → 100644
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wrappers/python/simtk/openmm/app/data/amber14/protein.ff15ipq.xml 0 → 100644
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wrappers/python/simtk/openmm/app/data/amber14/spce.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_spce" md5hash="576c159afdaa5f4f6b05250ce4326bd3" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_spce</Source>
<Source Source="parm/frcmod.ions234lm_126_spce" md5hash="11ef85dfcf07639646dd361590b76166" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_spce</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="spce.xml" md5hash="5c815beccd16958666face51044e4a7b" sourcePackage="OpenMM" sourcePackageVersion="7.2">spce.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Berendsen, H.J.C., Grigera, J.R., and Straatsma, T.P. (1987). The missing term in effective pair potentials. J. Phys. Chem. 91, 6269-6271.</Reference>
</Info>
<AtomTypes>
<Type class="spce_standard-Li+" element="Li" mass="6.94" name="spce_standard-Li+"/>
<Type class="spce_standard-Na+" element="Na" mass="22.99" name="spce_standard-Na+"/>
<Type class="spce_standard-K+" element="K" mass="39.1" name="spce_standard-K+"/>
<Type class="spce_standard-Rb+" element="Rb" mass="85.47" name="spce_standard-Rb+"/>
<Type class="spce_standard-Cs+" element="Cs" mass="132.91" name="spce_standard-Cs+"/>
<Type class="spce_standard-F-" element="F" mass="19.0" name="spce_standard-F-"/>
<Type class="spce_standard-Cl-" element="Cl" mass="35.45" name="spce_standard-Cl-"/>
<Type class="spce_standard-Br-" element="Br" mass="79.9" name="spce_standard-Br-"/>
<Type class="spce_standard-I-" element="I" mass="126.9" name="spce_standard-I-"/>
<Type class="spce_standard-Be2+" element="Be" mass="9.01" name="spce_standard-Be2+"/>
<Type class="spce_standard-Cu2+" element="Cu" mass="63.55" name="spce_standard-Cu2+"/>
<Type class="spce_standard-Ni2+" element="Ni" mass="58.69" name="spce_standard-Ni2+"/>
<Type class="spce_standard-Pt2+" element="Pt" mass="195.08" name="spce_standard-Pt2+"/>
<Type class="spce_standard-Zn2+" element="Zn" mass="65.4" name="spce_standard-Zn2+"/>
<Type class="spce_standard-Co2+" element="Co" mass="58.93" name="spce_standard-Co2+"/>
<Type class="spce_standard-Pd2+" element="Pd" mass="106.42" name="spce_standard-Pd2+"/>
<Type class="spce_standard-Ag2+" element="Ag" mass="107.87" name="spce_standard-Ag2+"/>
<Type class="spce_standard-Cr2+" element="Cr" mass="52.0" name="spce_standard-Cr2+"/>
<Type class="spce_standard-Fe2+" element="Fe" mass="55.85" name="spce_standard-Fe2+"/>
<Type class="spce_standard-Mg2+" element="Mg" mass="24.305" name="spce_standard-Mg2+"/>
<Type class="spce_standard-V2+" element="V" mass="50.94" name="spce_standard-V2+"/>
<Type class="spce_standard-Mn2+" element="Mn" mass="54.94" name="spce_standard-Mn2+"/>
<Type class="spce_standard-Hg2+" element="Hg" mass="200.59" name="spce_standard-Hg2+"/>
<Type class="spce_standard-Cd2+" element="Cd" mass="112.41" name="spce_standard-Cd2+"/>
<Type class="spce_standard-Yb2+" element="Yb" mass="173.05" name="spce_standard-Yb2+"/>
<Type class="spce_standard-Ca2+" element="Ca" mass="40.08" name="spce_standard-Ca2+"/>
<Type class="spce_standard-Sn2+" element="Sn" mass="118.71" name="spce_standard-Sn2+"/>
<Type class="spce_standard-Pb2+" element="Pb" mass="207.2" name="spce_standard-Pb2+"/>
<Type class="spce_standard-Eu2+" element="Eu" mass="151.96" name="spce_standard-Eu2+"/>
<Type class="spce_standard-Sr2+" element="Sr" mass="87.62" name="spce_standard-Sr2+"/>
<Type class="spce_standard-Sm2+" element="Sm" mass="150.36" name="spce_standard-Sm2+"/>
<Type class="spce_standard-Ba2+" element="Ba" mass="137.33" name="spce_standard-Ba2+"/>
<Type class="spce_standard-Ra2+" element="Ra" mass="226.03" name="spce_standard-Ra2+"/>
<Type class="spce_standard-Al3+" element="Al" mass="26.98" name="spce_standard-Al3+"/>
<Type class="spce_standard-Fe3+" element="Fe" mass="55.85" name="spce_standard-Fe3+"/>
<Type class="spce_standard-Cr3+" element="Cr" mass="52.0" name="spce_standard-Cr3+"/>
<Type class="spce_standard-In3+" element="In" mass="114.82" name="spce_standard-In3+"/>
<Type class="spce_standard-Tl3+" element="Tl" mass="204.38" name="spce_standard-Tl3+"/>
<Type class="spce_standard-Y3+" element="Y" mass="88.91" name="spce_standard-Y3+"/>
<Type class="spce_standard-La3+" element="La" mass="138.91" name="spce_standard-La3+"/>
<Type class="spce_standard-Ce3+" element="Ce" mass="140.12" name="spce_standard-Ce3+"/>
<Type class="spce_standard-Pr3+" element="Pr" mass="140.91" name="spce_standard-Pr3+"/>
<Type class="spce_standard-Nd3+" element="Nd" mass="144.24" name="spce_standard-Nd3+"/>
<Type class="spce_standard-Sm3+" element="Sm" mass="150.36" name="spce_standard-Sm3+"/>
<Type class="spce_standard-Eu3+" element="Eu" mass="151.96" name="spce_standard-Eu3+"/>
<Type class="spce_standard-Gd3+" element="Gd" mass="157.25" name="spce_standard-Gd3+"/>
<Type class="spce_standard-Tb3+" element="Tb" mass="158.93" name="spce_standard-Tb3+"/>
<Type class="spce_standard-Dy3+" element="Dy" mass="162.5" name="spce_standard-Dy3+"/>
<Type class="spce_standard-Er3+" element="Er" mass="167.26" name="spce_standard-Er3+"/>
<Type class="spce_standard-Tm3+" element="Tm" mass="168.93" name="spce_standard-Tm3+"/>
<Type class="spce_standard-Lu3+" element="Lu" mass="174.97" name="spce_standard-Lu3+"/>
<Type class="spce_standard-Hf4+" element="Hf" mass="178.49" name="spce_standard-Hf4+"/>
<Type class="spce_standard-Zr4+" element="Zr" mass="91.22" name="spce_standard-Zr4+"/>
<Type class="spce_standard-Ce4+" element="Ce" mass="140.12" name="spce_standard-Ce4+"/>
<Type class="spce_standard-U4+" element="U" mass="238.03" name="spce_standard-U4+"/>
<Type class="spce_standard-Pu4+" element="Pu" mass="244.06" name="spce_standard-Pu4+"/>
<Type class="spce_standard-Th4+" element="Th" mass="232.04" name="spce_standard-Th4+"/>
<Type name="spce-O" class="spce-O" element="O" mass="15.99943"/>
<Type name="spce-H" class="spce-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="spce_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="spce_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="spce_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="spce_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="spce_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="spce_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="spce_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="spce_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="spce_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="spce_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="spce_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="spce_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="spce_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="spce_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="spce_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="spce_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="spce_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="spce_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="spce_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="spce_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="spce_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="spce_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="spce_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="spce_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="spce_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="spce_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="spce_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="spce_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="spce_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="spce_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="spce_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="spce_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="spce_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="spce_standard-Na+"/>
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<Residue name="NI">
<Atom charge="2.0" name="NI" type="spce_standard-Ni2+"/>
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<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="spce_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="spce_standard-Pb2+"/>
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<Residue name="PD">
<Atom charge="2.0" name="PD" type="spce_standard-Pd2+"/>
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<Residue name="PR">
<Atom charge="3.0" name="PR" type="spce_standard-Pr3+"/>
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<Residue name="PT">
<Atom charge="2.0" name="PT" type="spce_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="spce_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="spce_standard-Rb+"/>
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<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="spce_standard-Ra2+"/>
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<Residue name="SM">
<Atom charge="3.0" name="SM" type="spce_standard-Sm3+"/>
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<Residue name="SR">
<Atom charge="2.0" name="SR" type="spce_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="spce_standard-Sm2+"/>
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<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="spce_standard-Sn2+"/>
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<Residue name="TB">
<Atom charge="3.0" name="TB" type="spce_standard-Tb3+"/>
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<Residue name="Th">
<Atom charge="4.0" name="Th" type="spce_standard-Th4+"/>
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<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="spce_standard-Tl3+"/>
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<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="spce_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="spce_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="spce_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="spce_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="spce_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="spce_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="spce_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="spce-O" charge="-0.8476"/>
<Atom name="H1" type="spce-H" charge="0.4238"/>
<Atom name="H2" type="spce-H" charge="0.4238"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="spce-O" type2="spce-H" length="0.1" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="spce-H" type2="spce-O" type3="spce-H" angle="1.91061193216" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="1.4088967296000001" sigma="0.14094017720980168" type="spce_standard-Li+"/>
<Atom epsilon="1.4754532912" sigma="0.21595384927721822" type="spce_standard-Na+"/>
<Atom epsilon="1.7978873936000002" sigma="0.2838403315995121" type="spce_standard-K+"/>
<Atom epsilon="1.8623134624" sigma="0.3094982146819539" type="spce_standard-Rb+"/>
<Atom epsilon="0.37595959600000006" sigma="0.36010126187232516" type="spce_standard-Cs+"/>
<Atom epsilon="0.030963692" sigma="0.4021516813685492" type="spce_standard-F-"/>
<Atom epsilon="0.05349244" sigma="0.48304528497569194" type="spce_standard-Cl-"/>
<Atom epsilon="0.1127947824" sigma="0.4901724747208147" type="spce_standard-Br-"/>
<Atom epsilon="0.179010348" sigma="0.5201066716503301" type="spce_standard-I-"/>
<Atom epsilon="1.92464e-05" sigma="0.1712307336265732" type="spce_standard-Be2+"/>
<Atom epsilon="0.0067303824" sigma="0.21791382645712698" type="spce_standard-Cu2+"/>
<Atom epsilon="0.01065702456" sigma="0.223259218765969" type="spce_standard-Ni2+"/>
<Atom epsilon="0.014015354" sigma="0.22664463389490233" type="spce_standard-Pt2+"/>
<Atom epsilon="0.014823368080000001" sigma="0.2273573528694146" type="spce_standard-Zn2+"/>
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="spce_standard-Co2+"/>
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="spce_standard-Pd2+"/>
<Atom epsilon="0.03264699888" sigma="0.23822631723072674" type="spce_standard-Ag2+"/>
<Atom epsilon="0.03718454688" sigma="0.2401862944106355" type="spce_standard-Cr2+"/>
<Atom epsilon="0.03986113536" sigma="0.2412553728724039" type="spce_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="spce_standard-Mg2+"/>
<Atom epsilon="0.045158958000000006" sigma="0.24321535005231262" type="spce_standard-V2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="spce_standard-Mn2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="spce_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="spce_standard-Cd2+"/>
<Atom epsilon="0.40718273784000003" sigma="0.2911457010882629" type="spce_standard-Yb2+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="spce_standard-Ca2+"/>
<Atom epsilon="0.44813803104000005" sigma="0.29417475672994003" type="spce_standard-Sn2+"/>
<Atom epsilon="0.669006956" sigma="0.3084291362201855" type="spce_standard-Pb2+"/>
<Atom epsilon="0.8445052544000001" sigma="0.31822902211972925" type="spce_standard-Eu2+"/>
<Atom epsilon="0.8713768270400001" sigma="0.31965446006875375" type="spce_standard-Sr2+"/>
<Atom epsilon="0.89173069" sigma="0.32072353853052216" type="spce_standard-Sm2+"/>
<Atom epsilon="1.55336865968" sigma="0.35279589238357434" type="spce_standard-Ba2+"/>
<Atom epsilon="1.55336865968" sigma="0.35279589238357434" type="spce_standard-Ra2+"/>
<Atom epsilon="0.019458696160000004" sigma="0.23092094774197594" type="spce_standard-Al3+"/>
<Atom epsilon="0.05678093848" sigma="0.24695712466850203" type="spce_standard-Fe3+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="spce_standard-Cr3+"/>
<Atom epsilon="0.11751709584" sigma="0.26032060544060714" type="spce_standard-In3+"/>
<Atom epsilon="0.18079185336" sigma="0.26958595210926667" type="spce_standard-Tl3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Y3+"/>
<Atom epsilon="0.63014479248" sigma="0.3061127995530206" type="spce_standard-La3+"/>
<Atom epsilon="0.69962078192" sigma="0.3102109336564662" type="spce_standard-Ce3+"/>
<Atom epsilon="0.6781265697600001" sigma="0.3089636754510697" type="spce_standard-Pr3+"/>
<Atom epsilon="0.52569060488" sigma="0.2995201490387821" type="spce_standard-Nd3+"/>
<Atom epsilon="0.46816830344000004" sigma="0.2956001946789646" type="spce_standard-Sm3+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="spce_standard-Eu3+"/>
<Atom epsilon="0.38186547936" sigma="0.2891857239083541" type="spce_standard-Gd3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="spce_standard-Tb3+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="spce_standard-Dy3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Er3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Tm3+"/>
<Atom epsilon="0.30760316128000004" sigma="0.28294943288137175" type="spce_standard-Lu3+"/>
<Atom epsilon="0.16448090592" sigma="0.26744779518572986" type="spce_standard-Hf4+"/>
<Atom epsilon="0.19225856560000001" sigma="0.2710113900582912" type="spce_standard-Zr4+"/>
<Atom epsilon="0.5474740988000001" sigma="0.3009455869878066" type="spce_standard-Ce4+"/>
<Atom epsilon="0.5474740988000001" sigma="0.3009455869878066" type="spce_standard-U4+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="spce_standard-Pu4+"/>
<Atom epsilon="0.61548811496" sigma="0.30522190083488027" type="spce_standard-Th4+"/>
<Atom type="spce-O" sigma="0.31657195050398818" epsilon="0.6497752"/>
<Atom type="spce-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/amber14/tip3p.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip3p" md5hash="0e5e74a17e42382511afd4116f70ff16" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip3p</Source>
<Source Source="parm/frcmod.ions234lm_126_tip3p" md5hash="69bb41a7702e76fb9f5ef041d063dfae" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip3p</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip3p.xml" md5hash="dde8c717e8d77c7511b575779ac9f968" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip3p.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., and Klein, M.L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 79, 926-935.</Reference>
</Info>
<AtomTypes>
<Type class="tip3p_standard-Li+" element="Li" mass="6.94" name="tip3p_standard-Li+"/>
<Type class="tip3p_standard-Na+" element="Na" mass="22.99" name="tip3p_standard-Na+"/>
<Type class="tip3p_standard-K+" element="K" mass="39.1" name="tip3p_standard-K+"/>
<Type class="tip3p_standard-Rb+" element="Rb" mass="85.47" name="tip3p_standard-Rb+"/>
<Type class="tip3p_standard-Cs+" element="Cs" mass="132.91" name="tip3p_standard-Cs+"/>
<Type class="tip3p_standard-F-" element="F" mass="19.0" name="tip3p_standard-F-"/>
<Type class="tip3p_standard-Cl-" element="Cl" mass="35.45" name="tip3p_standard-Cl-"/>
<Type class="tip3p_standard-Br-" element="Br" mass="79.9" name="tip3p_standard-Br-"/>
<Type class="tip3p_standard-I-" element="I" mass="126.9" name="tip3p_standard-I-"/>
<Type class="tip3p_standard-Be2+" element="Be" mass="9.01" name="tip3p_standard-Be2+"/>
<Type class="tip3p_standard-Cu2+" element="Cu" mass="63.55" name="tip3p_standard-Cu2+"/>
<Type class="tip3p_standard-Ni2+" element="Ni" mass="58.69" name="tip3p_standard-Ni2+"/>
<Type class="tip3p_standard-Pt2+" element="Pt" mass="195.08" name="tip3p_standard-Pt2+"/>
<Type class="tip3p_standard-Zn2+" element="Zn" mass="65.4" name="tip3p_standard-Zn2+"/>
<Type class="tip3p_standard-Co2+" element="Co" mass="58.93" name="tip3p_standard-Co2+"/>
<Type class="tip3p_standard-Pd2+" element="Pd" mass="106.42" name="tip3p_standard-Pd2+"/>
<Type class="tip3p_standard-Ag2+" element="Ag" mass="107.87" name="tip3p_standard-Ag2+"/>
<Type class="tip3p_standard-Cr2+" element="Cr" mass="52.0" name="tip3p_standard-Cr2+"/>
<Type class="tip3p_standard-Fe2+" element="Fe" mass="55.85" name="tip3p_standard-Fe2+"/>
<Type class="tip3p_standard-Mg2+" element="Mg" mass="24.305" name="tip3p_standard-Mg2+"/>
<Type class="tip3p_standard-V2+" element="V" mass="50.94" name="tip3p_standard-V2+"/>
<Type class="tip3p_standard-Mn2+" element="Mn" mass="54.94" name="tip3p_standard-Mn2+"/>
<Type class="tip3p_standard-Hg2+" element="Hg" mass="200.59" name="tip3p_standard-Hg2+"/>
<Type class="tip3p_standard-Cd2+" element="Cd" mass="112.41" name="tip3p_standard-Cd2+"/>
<Type class="tip3p_standard-Yb2+" element="Yb" mass="173.05" name="tip3p_standard-Yb2+"/>
<Type class="tip3p_standard-Ca2+" element="Ca" mass="40.08" name="tip3p_standard-Ca2+"/>
<Type class="tip3p_standard-Sn2+" element="Sn" mass="118.71" name="tip3p_standard-Sn2+"/>
<Type class="tip3p_standard-Pb2+" element="Pb" mass="207.2" name="tip3p_standard-Pb2+"/>
<Type class="tip3p_standard-Eu2+" element="Eu" mass="151.96" name="tip3p_standard-Eu2+"/>
<Type class="tip3p_standard-Sr2+" element="Sr" mass="87.62" name="tip3p_standard-Sr2+"/>
<Type class="tip3p_standard-Sm2+" element="Sm" mass="150.36" name="tip3p_standard-Sm2+"/>
<Type class="tip3p_standard-Ba2+" element="Ba" mass="137.33" name="tip3p_standard-Ba2+"/>
<Type class="tip3p_standard-Ra2+" element="Ra" mass="226.03" name="tip3p_standard-Ra2+"/>
<Type class="tip3p_standard-Al3+" element="Al" mass="26.98" name="tip3p_standard-Al3+"/>
<Type class="tip3p_standard-Fe3+" element="Fe" mass="55.85" name="tip3p_standard-Fe3+"/>
<Type class="tip3p_standard-Cr3+" element="Cr" mass="52.0" name="tip3p_standard-Cr3+"/>
<Type class="tip3p_standard-In3+" element="In" mass="114.82" name="tip3p_standard-In3+"/>
<Type class="tip3p_standard-Tl3+" element="Tl" mass="204.38" name="tip3p_standard-Tl3+"/>
<Type class="tip3p_standard-Y3+" element="Y" mass="88.91" name="tip3p_standard-Y3+"/>
<Type class="tip3p_standard-La3+" element="La" mass="138.91" name="tip3p_standard-La3+"/>
<Type class="tip3p_standard-Ce3+" element="Ce" mass="140.12" name="tip3p_standard-Ce3+"/>
<Type class="tip3p_standard-Pr3+" element="Pr" mass="140.91" name="tip3p_standard-Pr3+"/>
<Type class="tip3p_standard-Nd3+" element="Nd" mass="144.24" name="tip3p_standard-Nd3+"/>
<Type class="tip3p_standard-Sm3+" element="Sm" mass="150.36" name="tip3p_standard-Sm3+"/>
<Type class="tip3p_standard-Eu3+" element="Eu" mass="151.96" name="tip3p_standard-Eu3+"/>
<Type class="tip3p_standard-Gd3+" element="Gd" mass="157.25" name="tip3p_standard-Gd3+"/>
<Type class="tip3p_standard-Tb3+" element="Tb" mass="158.93" name="tip3p_standard-Tb3+"/>
<Type class="tip3p_standard-Dy3+" element="Dy" mass="162.5" name="tip3p_standard-Dy3+"/>
<Type class="tip3p_standard-Er3+" element="Er" mass="167.26" name="tip3p_standard-Er3+"/>
<Type class="tip3p_standard-Tm3+" element="Tm" mass="168.93" name="tip3p_standard-Tm3+"/>
<Type class="tip3p_standard-Lu3+" element="Lu" mass="174.97" name="tip3p_standard-Lu3+"/>
<Type class="tip3p_standard-Hf4+" element="Hf" mass="178.49" name="tip3p_standard-Hf4+"/>
<Type class="tip3p_standard-Zr4+" element="Zr" mass="91.22" name="tip3p_standard-Zr4+"/>
<Type class="tip3p_standard-Ce4+" element="Ce" mass="140.12" name="tip3p_standard-Ce4+"/>
<Type class="tip3p_standard-U4+" element="U" mass="238.03" name="tip3p_standard-U4+"/>
<Type class="tip3p_standard-Pu4+" element="Pu" mass="244.06" name="tip3p_standard-Pu4+"/>
<Type class="tip3p_standard-Th4+" element="Th" mass="232.04" name="tip3p_standard-Th4+"/>
<Type name="tip3p-O" class="tip3p-O" element="O" mass="15.99943"/>
<Type name="tip3p-H" class="tip3p-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip3p_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip3p_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip3p_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip3p_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip3p_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip3p_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip3p_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip3p_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip3p_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip3p_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip3p_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip3p_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip3p_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip3p_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip3p_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip3p_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip3p_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip3p_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip3p_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip3p_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip3p_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip3p_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip3p_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip3p_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip3p_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip3p_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip3p_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip3p_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip3p_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip3p_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip3p_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip3p_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip3p_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip3p_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip3p_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip3p_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip3p_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip3p_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip3p_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip3p_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip3p_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip3p_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip3p_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip3p_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip3p_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip3p_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip3p_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip3p_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip3p_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip3p_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip3p_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip3p_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip3p_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip3p_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip3p_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip3p_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip3p_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip3p-O" charge="-0.834"/>
<Atom name="H1" type="tip3p-H" charge="0.417"/>
<Atom name="H2" type="tip3p-H" charge="0.417"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip3p-O" type2="tip3p-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip3p-H" type2="tip3p-O" type3="tip3p-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.1171084864" sigma="0.18263423721876956" type="tip3p_standard-Li+"/>
<Atom epsilon="0.3658460312" sigma="0.2439280690268249" type="tip3p_standard-Na+"/>
<Atom epsilon="0.8103692536" sigma="0.3037964628858557" type="tip3p_standard-K+"/>
<Atom epsilon="1.3716068296000001" sigma="0.32303987519768707" type="tip3p_standard-Rb+"/>
<Atom epsilon="1.7009608496" sigma="0.3520831734090621" type="tip3p_standard-Cs+"/>
<Atom epsilon="0.014074976" sigma="0.4103479495754403" type="tip3p_standard-F-"/>
<Atom epsilon="0.14891274399999999" sigma="0.4477656957373345" type="tip3p_standard-Cl-"/>
<Atom epsilon="0.24541419360000002" sigma="0.46469277138200105" type="tip3p_standard-Br-"/>
<Atom epsilon="0.22460381440000002" sigma="0.5095940667762741" type="tip3p_standard-I-"/>
<Atom epsilon="1.6526800000000002e-05" sigma="0.17033983490843285" type="tip3p_standard-Be2+"/>
<Atom epsilon="0.00621311448" sigma="0.21702292773898668" type="tip3p_standard-Cu2+"/>
<Atom epsilon="0.0109754688" sigma="0.22361557825322517" type="tip3p_standard-Ni2+"/>
<Atom epsilon="0.01287174128" sigma="0.22557555543313393" type="tip3p_standard-Pt2+"/>
<Atom epsilon="0.01381916624" sigma="0.22646645415127425" type="tip3p_standard-Zn2+"/>
<Atom epsilon="0.02024604128" sigma="0.23145548697286014" type="tip3p_standard-Co2+"/>
<Atom epsilon="0.021335931440000004" sigma="0.23216820594737242" type="tip3p_standard-Pd2+"/>
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="tip3p_standard-Ag2+"/>
<Atom epsilon="0.03632456752" sigma="0.23982993492337937" type="tip3p_standard-Cr2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip3p_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="tip3p_standard-Mg2+"/>
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="tip3p_standard-V2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3p_standard-Mn2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3p_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="tip3p_standard-Cd2+"/>
<Atom epsilon="0.426181194" sigma="0.29257113903728743" type="tip3p_standard-Yb2+"/>
<Atom epsilon="0.4432056808" sigma="0.29381839724268394" type="tip3p_standard-Ca2+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="tip3p_standard-Sn2+"/>
<Atom epsilon="0.71203621616" sigma="0.31092365263097843" type="tip3p_standard-Pb2+"/>
<Atom epsilon="0.8985523254400001" sigma="0.3210798980177783" type="tip3p_standard-Eu2+"/>
<Atom epsilon="0.92601852816" sigma="0.32250533596680286" type="tip3p_standard-Sr2+"/>
<Atom epsilon="0.95724882464" sigma="0.32410895365945547" type="tip3p_standard-Sm2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3p_standard-Ba2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3p_standard-Ra2+"/>
<Atom epsilon="0.04721589608000001" sigma="0.2439280690268249" type="tip3p_standard-Al3+"/>
<Atom epsilon="0.09989325104" sigma="0.25711337005530194" type="tip3p_standard-Fe3+"/>
<Atom epsilon="0.07644268416000001" sigma="0.252124337233716" type="tip3p_standard-Cr3+"/>
<Atom epsilon="0.15168878616" sigma="0.2656659977494492" type="tip3p_standard-In3+"/>
<Atom epsilon="0.27501557520000003" sigma="0.2799203772396946" type="tip3p_standard-Tl3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="tip3p_standard-Y3+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip3p_standard-La3+"/>
<Atom epsilon="0.83118754056" sigma="0.31751630314521695" type="tip3p_standard-Ce3+"/>
<Atom epsilon="0.8245589130400001" sigma="0.31715994365796085" type="tip3p_standard-Pr3+"/>
<Atom epsilon="0.64794725224" sigma="0.307181878014789" type="tip3p_standard-Nd3+"/>
<Atom epsilon="0.60967151816" sigma="0.3048655413476241" type="tip3p_standard-Sm3+"/>
<Atom epsilon="0.62426246504" sigma="0.3057564400657644" type="tip3p_standard-Eu3+"/>
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="tip3p_standard-Gd3+"/>
<Atom epsilon="0.4991058036" sigma="0.2977383516025014" type="tip3p_standard-Tb3+"/>
<Atom epsilon="0.41424963936000003" sigma="0.29168024031914713" type="tip3p_standard-Dy3+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="tip3p_standard-Er3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip3p_standard-Tm3+"/>
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="tip3p_standard-Lu3+"/>
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="tip3p_standard-Hf4+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="tip3p_standard-Zr4+"/>
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="tip3p_standard-Ce4+"/>
<Atom epsilon="0.8646299178400001" sigma="0.31929810058149766" type="tip3p_standard-U4+"/>
<Atom epsilon="0.73399083568" sigma="0.3121709108363749" type="tip3p_standard-Pu4+"/>
<Atom epsilon="0.7917259353600001" sigma="0.31537814622168014" type="tip3p_standard-Th4+"/>
<Atom type="tip3p-O" sigma="0.31507524065751241" epsilon="0.635968"/>
<Atom type="tip3p-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/amber14/tip3pfb.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip3p" md5hash="0e5e74a17e42382511afd4116f70ff16" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip3p</Source>
<Source Source="parm/frcmod.ions234lm_126_tip3p" md5hash="69bb41a7702e76fb9f5ef041d063dfae" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip3p</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip3pfb.xml" md5hash="a7d1cb77f6a2d5ae69d7cd2b29bdfbf7" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip3pfb.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. (2014). Building force fields - an automatic, systematic and reproducible approach. Journal of Physical Chemistry Letters, 5, 1885-1891.</Reference>
</Info>
<AtomTypes>
<Type class="tip3pfb_standard-Li+" element="Li" mass="6.94" name="tip3pfb_standard-Li+"/>
<Type class="tip3pfb_standard-Na+" element="Na" mass="22.99" name="tip3pfb_standard-Na+"/>
<Type class="tip3pfb_standard-K+" element="K" mass="39.1" name="tip3pfb_standard-K+"/>
<Type class="tip3pfb_standard-Rb+" element="Rb" mass="85.47" name="tip3pfb_standard-Rb+"/>
<Type class="tip3pfb_standard-Cs+" element="Cs" mass="132.91" name="tip3pfb_standard-Cs+"/>
<Type class="tip3pfb_standard-F-" element="F" mass="19.0" name="tip3pfb_standard-F-"/>
<Type class="tip3pfb_standard-Cl-" element="Cl" mass="35.45" name="tip3pfb_standard-Cl-"/>
<Type class="tip3pfb_standard-Br-" element="Br" mass="79.9" name="tip3pfb_standard-Br-"/>
<Type class="tip3pfb_standard-I-" element="I" mass="126.9" name="tip3pfb_standard-I-"/>
<Type class="tip3pfb_standard-Be2+" element="Be" mass="9.01" name="tip3pfb_standard-Be2+"/>
<Type class="tip3pfb_standard-Cu2+" element="Cu" mass="63.55" name="tip3pfb_standard-Cu2+"/>
<Type class="tip3pfb_standard-Ni2+" element="Ni" mass="58.69" name="tip3pfb_standard-Ni2+"/>
<Type class="tip3pfb_standard-Pt2+" element="Pt" mass="195.08" name="tip3pfb_standard-Pt2+"/>
<Type class="tip3pfb_standard-Zn2+" element="Zn" mass="65.4" name="tip3pfb_standard-Zn2+"/>
<Type class="tip3pfb_standard-Co2+" element="Co" mass="58.93" name="tip3pfb_standard-Co2+"/>
<Type class="tip3pfb_standard-Pd2+" element="Pd" mass="106.42" name="tip3pfb_standard-Pd2+"/>
<Type class="tip3pfb_standard-Ag2+" element="Ag" mass="107.87" name="tip3pfb_standard-Ag2+"/>
<Type class="tip3pfb_standard-Cr2+" element="Cr" mass="52.0" name="tip3pfb_standard-Cr2+"/>
<Type class="tip3pfb_standard-Fe2+" element="Fe" mass="55.85" name="tip3pfb_standard-Fe2+"/>
<Type class="tip3pfb_standard-Mg2+" element="Mg" mass="24.305" name="tip3pfb_standard-Mg2+"/>
<Type class="tip3pfb_standard-V2+" element="V" mass="50.94" name="tip3pfb_standard-V2+"/>
<Type class="tip3pfb_standard-Mn2+" element="Mn" mass="54.94" name="tip3pfb_standard-Mn2+"/>
<Type class="tip3pfb_standard-Hg2+" element="Hg" mass="200.59" name="tip3pfb_standard-Hg2+"/>
<Type class="tip3pfb_standard-Cd2+" element="Cd" mass="112.41" name="tip3pfb_standard-Cd2+"/>
<Type class="tip3pfb_standard-Yb2+" element="Yb" mass="173.05" name="tip3pfb_standard-Yb2+"/>
<Type class="tip3pfb_standard-Ca2+" element="Ca" mass="40.08" name="tip3pfb_standard-Ca2+"/>
<Type class="tip3pfb_standard-Sn2+" element="Sn" mass="118.71" name="tip3pfb_standard-Sn2+"/>
<Type class="tip3pfb_standard-Pb2+" element="Pb" mass="207.2" name="tip3pfb_standard-Pb2+"/>
<Type class="tip3pfb_standard-Eu2+" element="Eu" mass="151.96" name="tip3pfb_standard-Eu2+"/>
<Type class="tip3pfb_standard-Sr2+" element="Sr" mass="87.62" name="tip3pfb_standard-Sr2+"/>
<Type class="tip3pfb_standard-Sm2+" element="Sm" mass="150.36" name="tip3pfb_standard-Sm2+"/>
<Type class="tip3pfb_standard-Ba2+" element="Ba" mass="137.33" name="tip3pfb_standard-Ba2+"/>
<Type class="tip3pfb_standard-Ra2+" element="Ra" mass="226.03" name="tip3pfb_standard-Ra2+"/>
<Type class="tip3pfb_standard-Al3+" element="Al" mass="26.98" name="tip3pfb_standard-Al3+"/>
<Type class="tip3pfb_standard-Fe3+" element="Fe" mass="55.85" name="tip3pfb_standard-Fe3+"/>
<Type class="tip3pfb_standard-Cr3+" element="Cr" mass="52.0" name="tip3pfb_standard-Cr3+"/>
<Type class="tip3pfb_standard-In3+" element="In" mass="114.82" name="tip3pfb_standard-In3+"/>
<Type class="tip3pfb_standard-Tl3+" element="Tl" mass="204.38" name="tip3pfb_standard-Tl3+"/>
<Type class="tip3pfb_standard-Y3+" element="Y" mass="88.91" name="tip3pfb_standard-Y3+"/>
<Type class="tip3pfb_standard-La3+" element="La" mass="138.91" name="tip3pfb_standard-La3+"/>
<Type class="tip3pfb_standard-Ce3+" element="Ce" mass="140.12" name="tip3pfb_standard-Ce3+"/>
<Type class="tip3pfb_standard-Pr3+" element="Pr" mass="140.91" name="tip3pfb_standard-Pr3+"/>
<Type class="tip3pfb_standard-Nd3+" element="Nd" mass="144.24" name="tip3pfb_standard-Nd3+"/>
<Type class="tip3pfb_standard-Sm3+" element="Sm" mass="150.36" name="tip3pfb_standard-Sm3+"/>
<Type class="tip3pfb_standard-Eu3+" element="Eu" mass="151.96" name="tip3pfb_standard-Eu3+"/>
<Type class="tip3pfb_standard-Gd3+" element="Gd" mass="157.25" name="tip3pfb_standard-Gd3+"/>
<Type class="tip3pfb_standard-Tb3+" element="Tb" mass="158.93" name="tip3pfb_standard-Tb3+"/>
<Type class="tip3pfb_standard-Dy3+" element="Dy" mass="162.5" name="tip3pfb_standard-Dy3+"/>
<Type class="tip3pfb_standard-Er3+" element="Er" mass="167.26" name="tip3pfb_standard-Er3+"/>
<Type class="tip3pfb_standard-Tm3+" element="Tm" mass="168.93" name="tip3pfb_standard-Tm3+"/>
<Type class="tip3pfb_standard-Lu3+" element="Lu" mass="174.97" name="tip3pfb_standard-Lu3+"/>
<Type class="tip3pfb_standard-Hf4+" element="Hf" mass="178.49" name="tip3pfb_standard-Hf4+"/>
<Type class="tip3pfb_standard-Zr4+" element="Zr" mass="91.22" name="tip3pfb_standard-Zr4+"/>
<Type class="tip3pfb_standard-Ce4+" element="Ce" mass="140.12" name="tip3pfb_standard-Ce4+"/>
<Type class="tip3pfb_standard-U4+" element="U" mass="238.03" name="tip3pfb_standard-U4+"/>
<Type class="tip3pfb_standard-Pu4+" element="Pu" mass="244.06" name="tip3pfb_standard-Pu4+"/>
<Type class="tip3pfb_standard-Th4+" element="Th" mass="232.04" name="tip3pfb_standard-Th4+"/>
<Type name="tip3p-fb-O" class="tip3p-fb-O" element="O" mass="15.99943"/>
<Type name="tip3p-fb-H" class="tip3p-fb-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip3pfb_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip3pfb_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip3pfb_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip3pfb_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip3pfb_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip3pfb_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip3pfb_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip3pfb_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip3pfb_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip3pfb_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip3pfb_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip3pfb_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip3pfb_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip3pfb_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip3pfb_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip3pfb_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip3pfb_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip3pfb_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip3pfb_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip3pfb_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip3pfb_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip3pfb_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip3pfb_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip3pfb_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip3pfb_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip3pfb_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip3pfb_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip3pfb_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip3pfb_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip3pfb_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip3pfb_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip3pfb_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip3pfb_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip3pfb_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip3pfb_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip3pfb_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip3pfb_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip3pfb_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip3pfb_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip3pfb_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip3pfb_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip3pfb_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip3pfb_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip3pfb_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip3pfb_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip3pfb_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip3pfb_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip3pfb_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip3pfb_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip3pfb_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip3pfb_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip3pfb_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip3pfb_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip3pfb_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip3pfb_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip3pfb_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip3pfb_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip3p-fb-O" charge="-0.848448690103"/>
<Atom name="H1" type="tip3p-fb-H" charge="0.4242243450515"/>
<Atom name="H2" type="tip3p-fb-H" charge="0.4242243450515"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip3p-fb-O" type2="tip3p-fb-H" length="0.101181082494" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip3p-fb-H" type2="tip3p-fb-O" type3="tip3p-fb-H" angle="1.88754640288" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.1171084864" sigma="0.18263423721876956" type="tip3pfb_standard-Li+"/>
<Atom epsilon="0.3658460312" sigma="0.2439280690268249" type="tip3pfb_standard-Na+"/>
<Atom epsilon="0.8103692536" sigma="0.3037964628858557" type="tip3pfb_standard-K+"/>
<Atom epsilon="1.3716068296000001" sigma="0.32303987519768707" type="tip3pfb_standard-Rb+"/>
<Atom epsilon="1.7009608496" sigma="0.3520831734090621" type="tip3pfb_standard-Cs+"/>
<Atom epsilon="0.014074976" sigma="0.4103479495754403" type="tip3pfb_standard-F-"/>
<Atom epsilon="0.14891274399999999" sigma="0.4477656957373345" type="tip3pfb_standard-Cl-"/>
<Atom epsilon="0.24541419360000002" sigma="0.46469277138200105" type="tip3pfb_standard-Br-"/>
<Atom epsilon="0.22460381440000002" sigma="0.5095940667762741" type="tip3pfb_standard-I-"/>
<Atom epsilon="1.6526800000000002e-05" sigma="0.17033983490843285" type="tip3pfb_standard-Be2+"/>
<Atom epsilon="0.00621311448" sigma="0.21702292773898668" type="tip3pfb_standard-Cu2+"/>
<Atom epsilon="0.0109754688" sigma="0.22361557825322517" type="tip3pfb_standard-Ni2+"/>
<Atom epsilon="0.01287174128" sigma="0.22557555543313393" type="tip3pfb_standard-Pt2+"/>
<Atom epsilon="0.01381916624" sigma="0.22646645415127425" type="tip3pfb_standard-Zn2+"/>
<Atom epsilon="0.02024604128" sigma="0.23145548697286014" type="tip3pfb_standard-Co2+"/>
<Atom epsilon="0.021335931440000004" sigma="0.23216820594737242" type="tip3pfb_standard-Pd2+"/>
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="tip3pfb_standard-Ag2+"/>
<Atom epsilon="0.03632456752" sigma="0.23982993492337937" type="tip3pfb_standard-Cr2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip3pfb_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="tip3pfb_standard-Mg2+"/>
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="tip3pfb_standard-V2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3pfb_standard-Mn2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3pfb_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="tip3pfb_standard-Cd2+"/>
<Atom epsilon="0.426181194" sigma="0.29257113903728743" type="tip3pfb_standard-Yb2+"/>
<Atom epsilon="0.4432056808" sigma="0.29381839724268394" type="tip3pfb_standard-Ca2+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="tip3pfb_standard-Sn2+"/>
<Atom epsilon="0.71203621616" sigma="0.31092365263097843" type="tip3pfb_standard-Pb2+"/>
<Atom epsilon="0.8985523254400001" sigma="0.3210798980177783" type="tip3pfb_standard-Eu2+"/>
<Atom epsilon="0.92601852816" sigma="0.32250533596680286" type="tip3pfb_standard-Sr2+"/>
<Atom epsilon="0.95724882464" sigma="0.32410895365945547" type="tip3pfb_standard-Sm2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3pfb_standard-Ba2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3pfb_standard-Ra2+"/>
<Atom epsilon="0.04721589608000001" sigma="0.2439280690268249" type="tip3pfb_standard-Al3+"/>
<Atom epsilon="0.09989325104" sigma="0.25711337005530194" type="tip3pfb_standard-Fe3+"/>
<Atom epsilon="0.07644268416000001" sigma="0.252124337233716" type="tip3pfb_standard-Cr3+"/>
<Atom epsilon="0.15168878616" sigma="0.2656659977494492" type="tip3pfb_standard-In3+"/>
<Atom epsilon="0.27501557520000003" sigma="0.2799203772396946" type="tip3pfb_standard-Tl3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="tip3pfb_standard-Y3+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip3pfb_standard-La3+"/>
<Atom epsilon="0.83118754056" sigma="0.31751630314521695" type="tip3pfb_standard-Ce3+"/>
<Atom epsilon="0.8245589130400001" sigma="0.31715994365796085" type="tip3pfb_standard-Pr3+"/>
<Atom epsilon="0.64794725224" sigma="0.307181878014789" type="tip3pfb_standard-Nd3+"/>
<Atom epsilon="0.60967151816" sigma="0.3048655413476241" type="tip3pfb_standard-Sm3+"/>
<Atom epsilon="0.62426246504" sigma="0.3057564400657644" type="tip3pfb_standard-Eu3+"/>
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="tip3pfb_standard-Gd3+"/>
<Atom epsilon="0.4991058036" sigma="0.2977383516025014" type="tip3pfb_standard-Tb3+"/>
<Atom epsilon="0.41424963936000003" sigma="0.29168024031914713" type="tip3pfb_standard-Dy3+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="tip3pfb_standard-Er3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip3pfb_standard-Tm3+"/>
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="tip3pfb_standard-Lu3+"/>
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="tip3pfb_standard-Hf4+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="tip3pfb_standard-Zr4+"/>
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="tip3pfb_standard-Ce4+"/>
<Atom epsilon="0.8646299178400001" sigma="0.31929810058149766" type="tip3pfb_standard-U4+"/>
<Atom epsilon="0.73399083568" sigma="0.3121709108363749" type="tip3pfb_standard-Pu4+"/>
<Atom epsilon="0.7917259353600001" sigma="0.31537814622168014" type="tip3pfb_standard-Th4+"/>
<Atom type="tip3p-fb-O" sigma="0.317796456355" epsilon="0.652143528104"/>
<Atom type="tip3p-fb-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/amber14/tip4pew.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip4pew" md5hash="7aa9de49a8df5ebc45f74e1f47d13c2a" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip4pew</Source>
<Source Source="parm/frcmod.ions234lm_126_tip4pew" md5hash="3902b775a0fe5d42cab716a82c183747" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip4pew</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip4pew.xml" md5hash="cb450d015f4c238271cef8825f5ad7bd" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip4pew.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279q13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Horn, H.W., Swope, W.C., Pitera, J.W., Madura, J.D., Dick, T.J., Hura, G.L., and Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics 120, 9665-9678.</Reference>
<Reference>Horn, H.W., Swope, W.C., and Pitera, J.W. (2005). Characterization of the TIP4P-Ew water model: Vapor pressure and boiling point. The Journal of Chemical Physics 123, 194504.</Reference>
</Info>
<AtomTypes>
<Type class="tip4pew_standard-Li+" element="Li" mass="6.94" name="tip4pew_standard-Li+"/>
<Type class="tip4pew_standard-Na+" element="Na" mass="22.99" name="tip4pew_standard-Na+"/>
<Type class="tip4pew_standard-K+" element="K" mass="39.1" name="tip4pew_standard-K+"/>
<Type class="tip4pew_standard-Rb+" element="Rb" mass="85.47" name="tip4pew_standard-Rb+"/>
<Type class="tip4pew_standard-Cs+" element="Cs" mass="132.91" name="tip4pew_standard-Cs+"/>
<Type class="tip4pew_standard-F-" element="F" mass="19.0" name="tip4pew_standard-F-"/>
<Type class="tip4pew_standard-Cl-" element="Cl" mass="35.45" name="tip4pew_standard-Cl-"/>
<Type class="tip4pew_standard-Br-" element="Br" mass="79.9" name="tip4pew_standard-Br-"/>
<Type class="tip4pew_standard-I-" element="I" mass="126.9" name="tip4pew_standard-I-"/>
<Type class="tip4pew_standard-Be2+" element="Be" mass="9.01" name="tip4pew_standard-Be2+"/>
<Type class="tip4pew_standard-Cu2+" element="Cu" mass="63.55" name="tip4pew_standard-Cu2+"/>
<Type class="tip4pew_standard-Ni2+" element="Ni" mass="58.69" name="tip4pew_standard-Ni2+"/>
<Type class="tip4pew_standard-Pt2+" element="Pt" mass="195.08" name="tip4pew_standard-Pt2+"/>
<Type class="tip4pew_standard-Zn2+" element="Zn" mass="65.4" name="tip4pew_standard-Zn2+"/>
<Type class="tip4pew_standard-Co2+" element="Co" mass="58.93" name="tip4pew_standard-Co2+"/>
<Type class="tip4pew_standard-Pd2+" element="Pd" mass="106.42" name="tip4pew_standard-Pd2+"/>
<Type class="tip4pew_standard-Ag2+" element="Ag" mass="107.87" name="tip4pew_standard-Ag2+"/>
<Type class="tip4pew_standard-Cr2+" element="Cr" mass="52.0" name="tip4pew_standard-Cr2+"/>
<Type class="tip4pew_standard-Fe2+" element="Fe" mass="55.85" name="tip4pew_standard-Fe2+"/>
<Type class="tip4pew_standard-Mg2+" element="Mg" mass="24.305" name="tip4pew_standard-Mg2+"/>
<Type class="tip4pew_standard-V2+" element="V" mass="50.94" name="tip4pew_standard-V2+"/>
<Type class="tip4pew_standard-Mn2+" element="Mn" mass="54.94" name="tip4pew_standard-Mn2+"/>
<Type class="tip4pew_standard-Hg2+" element="Hg" mass="200.59" name="tip4pew_standard-Hg2+"/>
<Type class="tip4pew_standard-Cd2+" element="Cd" mass="112.41" name="tip4pew_standard-Cd2+"/>
<Type class="tip4pew_standard-Yb2+" element="Yb" mass="173.05" name="tip4pew_standard-Yb2+"/>
<Type class="tip4pew_standard-Ca2+" element="Ca" mass="40.08" name="tip4pew_standard-Ca2+"/>
<Type class="tip4pew_standard-Sn2+" element="Sn" mass="118.71" name="tip4pew_standard-Sn2+"/>
<Type class="tip4pew_standard-Pb2+" element="Pb" mass="207.2" name="tip4pew_standard-Pb2+"/>
<Type class="tip4pew_standard-Eu2+" element="Eu" mass="151.96" name="tip4pew_standard-Eu2+"/>
<Type class="tip4pew_standard-Sr2+" element="Sr" mass="87.62" name="tip4pew_standard-Sr2+"/>
<Type class="tip4pew_standard-Sm2+" element="Sm" mass="150.36" name="tip4pew_standard-Sm2+"/>
<Type class="tip4pew_standard-Ba2+" element="Ba" mass="137.33" name="tip4pew_standard-Ba2+"/>
<Type class="tip4pew_standard-Ra2+" element="Ra" mass="226.03" name="tip4pew_standard-Ra2+"/>
<Type class="tip4pew_standard-Al3+" element="Al" mass="26.98" name="tip4pew_standard-Al3+"/>
<Type class="tip4pew_standard-Fe3+" element="Fe" mass="55.85" name="tip4pew_standard-Fe3+"/>
<Type class="tip4pew_standard-Cr3+" element="Cr" mass="52.0" name="tip4pew_standard-Cr3+"/>
<Type class="tip4pew_standard-In3+" element="In" mass="114.82" name="tip4pew_standard-In3+"/>
<Type class="tip4pew_standard-Tl3+" element="Tl" mass="204.38" name="tip4pew_standard-Tl3+"/>
<Type class="tip4pew_standard-Y3+" element="Y" mass="88.91" name="tip4pew_standard-Y3+"/>
<Type class="tip4pew_standard-La3+" element="La" mass="138.91" name="tip4pew_standard-La3+"/>
<Type class="tip4pew_standard-Ce3+" element="Ce" mass="140.12" name="tip4pew_standard-Ce3+"/>
<Type class="tip4pew_standard-Pr3+" element="Pr" mass="140.91" name="tip4pew_standard-Pr3+"/>
<Type class="tip4pew_standard-Nd3+" element="Nd" mass="144.24" name="tip4pew_standard-Nd3+"/>
<Type class="tip4pew_standard-Sm3+" element="Sm" mass="150.36" name="tip4pew_standard-Sm3+"/>
<Type class="tip4pew_standard-Eu3+" element="Eu" mass="151.96" name="tip4pew_standard-Eu3+"/>
<Type class="tip4pew_standard-Gd3+" element="Gd" mass="157.25" name="tip4pew_standard-Gd3+"/>
<Type class="tip4pew_standard-Tb3+" element="Tb" mass="158.93" name="tip4pew_standard-Tb3+"/>
<Type class="tip4pew_standard-Dy3+" element="Dy" mass="162.5" name="tip4pew_standard-Dy3+"/>
<Type class="tip4pew_standard-Er3+" element="Er" mass="167.26" name="tip4pew_standard-Er3+"/>
<Type class="tip4pew_standard-Tm3+" element="Tm" mass="168.93" name="tip4pew_standard-Tm3+"/>
<Type class="tip4pew_standard-Lu3+" element="Lu" mass="174.97" name="tip4pew_standard-Lu3+"/>
<Type class="tip4pew_standard-Hf4+" element="Hf" mass="178.49" name="tip4pew_standard-Hf4+"/>
<Type class="tip4pew_standard-Zr4+" element="Zr" mass="91.22" name="tip4pew_standard-Zr4+"/>
<Type class="tip4pew_standard-Ce4+" element="Ce" mass="140.12" name="tip4pew_standard-Ce4+"/>
<Type class="tip4pew_standard-U4+" element="U" mass="238.03" name="tip4pew_standard-U4+"/>
<Type class="tip4pew_standard-Pu4+" element="Pu" mass="244.06" name="tip4pew_standard-Pu4+"/>
<Type class="tip4pew_standard-Th4+" element="Th" mass="232.04" name="tip4pew_standard-Th4+"/>
<Type name="tip4pew-O" class="tip4pew-O" element="O" mass="15.99943"/>
<Type name="tip4pew-H" class="tip4pew-H" element="H" mass="1.007947"/>
<Type name="tip4pew-M" class="tip4pew-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip4pew_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip4pew_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip4pew_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip4pew_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip4pew_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip4pew_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip4pew_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip4pew_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip4pew_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip4pew_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip4pew_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip4pew_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip4pew_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip4pew_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip4pew_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip4pew_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip4pew_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip4pew_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip4pew_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip4pew_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip4pew_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip4pew_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip4pew_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip4pew_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip4pew_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip4pew_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip4pew_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip4pew_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip4pew_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip4pew_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip4pew_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip4pew_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip4pew_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip4pew_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip4pew_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip4pew_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip4pew_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip4pew_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip4pew_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip4pew_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip4pew_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip4pew_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip4pew_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip4pew_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip4pew_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip4pew_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip4pew_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip4pew_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip4pew_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip4pew_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip4pew_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip4pew_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip4pew_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip4pew_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip4pew_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip4pew_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip4pew_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip4pew-O" charge="0"/>
<Atom name="H1" type="tip4pew-H" charge="0.52422"/>
<Atom name="H2" type="tip4pew-H" charge="0.52422"/>
<Atom name="M" type="tip4pew-M" charge="-1.04844"/>
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip4pew-O" type2="tip4pew-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip4pew-H" type2="tip4pew-O" type3="tip4pew-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.4350874656" sigma="0.14396923285147886" type="tip4pew_standard-Li+"/>
<Atom epsilon="0.7047424999999999" sigma="0.21844836568801118" type="tip4pew_standard-Na+"/>
<Atom epsilon="1.1692819784000001" sigma="0.2833057923686279" type="tip4pew_standard-K+"/>
<Atom epsilon="1.8122970896000001" sigma="0.304509181860368" type="tip4pew_standard-Rb+"/>
<Atom epsilon="1.6503026512" sigma="0.3364033559697921" type="tip4pew_standard-Cs+"/>
<Atom epsilon="0.0065906368" sigma="0.4522201893280362" type="tip4pew_standard-F-"/>
<Atom epsilon="0.048791716" sigma="0.49177609241346726" type="tip4pew_standard-Cl-"/>
<Atom epsilon="0.1270986232" sigma="0.4932015303624918" type="tip4pew_standard-Br-"/>
<Atom epsilon="0.1745071088" sigma="0.5259866031900563" type="tip4pew_standard-I-"/>
<Atom epsilon="4.853439999999999e-06" sigma="0.1635690046505663" type="tip4pew_standard-Be2+"/>
<Atom epsilon="0.00424537928" sigma="0.2129247936355411" type="tip4pew_standard-Cu2+"/>
<Atom epsilon="0.00651925776" sigma="0.21755746696987088" type="tip4pew_standard-Ni2+"/>
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="tip4pew_standard-Pt2+"/>
<Atom epsilon="0.01050071032" sigma="0.22308103902234097" type="tip4pew_standard-Zn2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pew_standard-Co2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pew_standard-Pd2+"/>
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="tip4pew_standard-Ag2+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pew_standard-Cr2+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="tip4pew_standard-Fe2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pew_standard-Mg2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pew_standard-V2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pew_standard-Mn2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pew_standard-Hg2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="tip4pew_standard-Cd2+"/>
<Atom epsilon="0.45559312408" sigma="0.29470929596082424" type="tip4pew_standard-Yb2+"/>
<Atom epsilon="0.46311578872000003" sigma="0.29524383519170844" type="tip4pew_standard-Ca2+"/>
<Atom epsilon="0.49648724720000004" sigma="0.29756017185887335" type="tip4pew_standard-Sn2+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip4pew_standard-Pb2+"/>
<Atom epsilon="0.9712365224" sigma="0.3248216726339677" type="tip4pew_standard-Eu2+"/>
<Atom epsilon="0.985288068" sigma="0.32553439160847997" type="tip4pew_standard-Sr2+"/>
<Atom epsilon="1.02424478992" sigma="0.3274943687883887" type="tip4pew_standard-Sm2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pew_standard-Ba2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pew_standard-Ra2+"/>
<Atom epsilon="0.01678206584" sigma="0.22896097056206718" type="tip4pew_standard-Al3+"/>
<Atom epsilon="0.05043699032" sigma="0.2449971474885933" type="tip4pew_standard-Fe3+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pew_standard-Cr3+"/>
<Atom epsilon="0.10650049832000001" sigma="0.2583606282606984" type="tip4pew_standard-In3+"/>
<Atom epsilon="0.16579982824" sigma="0.2676259749293579" type="tip4pew_standard-Tl3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Y3+"/>
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="tip4pew_standard-La3+"/>
<Atom epsilon="0.66295839824" sigma="0.3080727767329294" type="tip4pew_standard-Ce3+"/>
<Atom epsilon="0.64198735344" sigma="0.30682551852753287" type="tip4pew_standard-Pr3+"/>
<Atom epsilon="0.49387597096" sigma="0.2973819921152453" type="tip4pew_standard-Nd3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip4pew_standard-Sm3+"/>
<Atom epsilon="0.4580931896" sigma="0.29488747570445234" type="tip4pew_standard-Eu3+"/>
<Atom epsilon="0.35748949536" sigma="0.2872257467284454" type="tip4pew_standard-Gd3+"/>
<Atom epsilon="0.37289213824" sigma="0.28847300493384187" type="tip4pew_standard-Tb3+"/>
<Atom epsilon="0.32577870832" sigma="0.28455305057402436" type="tip4pew_standard-Dy3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Er3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Tm3+"/>
<Atom epsilon="0.28625681168" sigma="0.280989455701463" type="tip4pew_standard-Lu3+"/>
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="tip4pew_standard-Hf4+"/>
<Atom epsilon="0.16712607256" sigma="0.26780415467298596" type="tip4pew_standard-Zr4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pew_standard-Ce4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pew_standard-U4+"/>
<Atom epsilon="0.43343181496" sigma="0.29310567826817163" type="tip4pew_standard-Pu4+"/>
<Atom epsilon="0.5502288444000001" sigma="0.3011237667314347" type="tip4pew_standard-Th4+"/>
<Atom type="tip4pew-O" sigma="0.316435" epsilon="0.680946"/>
<Atom type="tip4pew-H" sigma="1" epsilon="0"/>
<Atom type="tip4pew-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/amber14/tip4pfb.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip4pew" md5hash="7aa9de49a8df5ebc45f74e1f47d13c2a" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip4pew</Source>
<Source Source="parm/frcmod.ions234lm_126_tip4pew" md5hash="3902b775a0fe5d42cab716a82c183747" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip4pew</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip4pfb.xml" md5hash="5da20fd20f6aefc31c499fc7c635bf69" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip4pfb.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279q13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. (2014). Building force fields - an automatic, systematic and reproducible approach. Journal of Physical Chemistry Letters, 5, 1885-1891.</Reference>
</Info>
<AtomTypes>
<Type class="tip4pfb_standard-Li+" element="Li" mass="6.94" name="tip4pfb_standard-Li+"/>
<Type class="tip4pfb_standard-Na+" element="Na" mass="22.99" name="tip4pfb_standard-Na+"/>
<Type class="tip4pfb_standard-K+" element="K" mass="39.1" name="tip4pfb_standard-K+"/>
<Type class="tip4pfb_standard-Rb+" element="Rb" mass="85.47" name="tip4pfb_standard-Rb+"/>
<Type class="tip4pfb_standard-Cs+" element="Cs" mass="132.91" name="tip4pfb_standard-Cs+"/>
<Type class="tip4pfb_standard-F-" element="F" mass="19.0" name="tip4pfb_standard-F-"/>
<Type class="tip4pfb_standard-Cl-" element="Cl" mass="35.45" name="tip4pfb_standard-Cl-"/>
<Type class="tip4pfb_standard-Br-" element="Br" mass="79.9" name="tip4pfb_standard-Br-"/>
<Type class="tip4pfb_standard-I-" element="I" mass="126.9" name="tip4pfb_standard-I-"/>
<Type class="tip4pfb_standard-Be2+" element="Be" mass="9.01" name="tip4pfb_standard-Be2+"/>
<Type class="tip4pfb_standard-Cu2+" element="Cu" mass="63.55" name="tip4pfb_standard-Cu2+"/>
<Type class="tip4pfb_standard-Ni2+" element="Ni" mass="58.69" name="tip4pfb_standard-Ni2+"/>
<Type class="tip4pfb_standard-Pt2+" element="Pt" mass="195.08" name="tip4pfb_standard-Pt2+"/>
<Type class="tip4pfb_standard-Zn2+" element="Zn" mass="65.4" name="tip4pfb_standard-Zn2+"/>
<Type class="tip4pfb_standard-Co2+" element="Co" mass="58.93" name="tip4pfb_standard-Co2+"/>
<Type class="tip4pfb_standard-Pd2+" element="Pd" mass="106.42" name="tip4pfb_standard-Pd2+"/>
<Type class="tip4pfb_standard-Ag2+" element="Ag" mass="107.87" name="tip4pfb_standard-Ag2+"/>
<Type class="tip4pfb_standard-Cr2+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr2+"/>
<Type class="tip4pfb_standard-Fe2+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe2+"/>
<Type class="tip4pfb_standard-Mg2+" element="Mg" mass="24.305" name="tip4pfb_standard-Mg2+"/>
<Type class="tip4pfb_standard-V2+" element="V" mass="50.94" name="tip4pfb_standard-V2+"/>
<Type class="tip4pfb_standard-Mn2+" element="Mn" mass="54.94" name="tip4pfb_standard-Mn2+"/>
<Type class="tip4pfb_standard-Hg2+" element="Hg" mass="200.59" name="tip4pfb_standard-Hg2+"/>
<Type class="tip4pfb_standard-Cd2+" element="Cd" mass="112.41" name="tip4pfb_standard-Cd2+"/>
<Type class="tip4pfb_standard-Yb2+" element="Yb" mass="173.05" name="tip4pfb_standard-Yb2+"/>
<Type class="tip4pfb_standard-Ca2+" element="Ca" mass="40.08" name="tip4pfb_standard-Ca2+"/>
<Type class="tip4pfb_standard-Sn2+" element="Sn" mass="118.71" name="tip4pfb_standard-Sn2+"/>
<Type class="tip4pfb_standard-Pb2+" element="Pb" mass="207.2" name="tip4pfb_standard-Pb2+"/>
<Type class="tip4pfb_standard-Eu2+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu2+"/>
<Type class="tip4pfb_standard-Sr2+" element="Sr" mass="87.62" name="tip4pfb_standard-Sr2+"/>
<Type class="tip4pfb_standard-Sm2+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm2+"/>
<Type class="tip4pfb_standard-Ba2+" element="Ba" mass="137.33" name="tip4pfb_standard-Ba2+"/>
<Type class="tip4pfb_standard-Ra2+" element="Ra" mass="226.03" name="tip4pfb_standard-Ra2+"/>
<Type class="tip4pfb_standard-Al3+" element="Al" mass="26.98" name="tip4pfb_standard-Al3+"/>
<Type class="tip4pfb_standard-Fe3+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe3+"/>
<Type class="tip4pfb_standard-Cr3+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr3+"/>
<Type class="tip4pfb_standard-In3+" element="In" mass="114.82" name="tip4pfb_standard-In3+"/>
<Type class="tip4pfb_standard-Tl3+" element="Tl" mass="204.38" name="tip4pfb_standard-Tl3+"/>
<Type class="tip4pfb_standard-Y3+" element="Y" mass="88.91" name="tip4pfb_standard-Y3+"/>
<Type class="tip4pfb_standard-La3+" element="La" mass="138.91" name="tip4pfb_standard-La3+"/>
<Type class="tip4pfb_standard-Ce3+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce3+"/>
<Type class="tip4pfb_standard-Pr3+" element="Pr" mass="140.91" name="tip4pfb_standard-Pr3+"/>
<Type class="tip4pfb_standard-Nd3+" element="Nd" mass="144.24" name="tip4pfb_standard-Nd3+"/>
<Type class="tip4pfb_standard-Sm3+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm3+"/>
<Type class="tip4pfb_standard-Eu3+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu3+"/>
<Type class="tip4pfb_standard-Gd3+" element="Gd" mass="157.25" name="tip4pfb_standard-Gd3+"/>
<Type class="tip4pfb_standard-Tb3+" element="Tb" mass="158.93" name="tip4pfb_standard-Tb3+"/>
<Type class="tip4pfb_standard-Dy3+" element="Dy" mass="162.5" name="tip4pfb_standard-Dy3+"/>
<Type class="tip4pfb_standard-Er3+" element="Er" mass="167.26" name="tip4pfb_standard-Er3+"/>
<Type class="tip4pfb_standard-Tm3+" element="Tm" mass="168.93" name="tip4pfb_standard-Tm3+"/>
<Type class="tip4pfb_standard-Lu3+" element="Lu" mass="174.97" name="tip4pfb_standard-Lu3+"/>
<Type class="tip4pfb_standard-Hf4+" element="Hf" mass="178.49" name="tip4pfb_standard-Hf4+"/>
<Type class="tip4pfb_standard-Zr4+" element="Zr" mass="91.22" name="tip4pfb_standard-Zr4+"/>
<Type class="tip4pfb_standard-Ce4+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce4+"/>
<Type class="tip4pfb_standard-U4+" element="U" mass="238.03" name="tip4pfb_standard-U4+"/>
<Type class="tip4pfb_standard-Pu4+" element="Pu" mass="244.06" name="tip4pfb_standard-Pu4+"/>
<Type class="tip4pfb_standard-Th4+" element="Th" mass="232.04" name="tip4pfb_standard-Th4+"/>
<Type name="tip4p-fb-O" class="tip4p-fb-O" element="O" mass="15.99943"/>
<Type name="tip4p-fb-H" class="tip4p-fb-H" element="H" mass="1.007947"/>
<Type name="tip4p-fb-M" class="tip4p-fb-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip4pfb_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip4pfb_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip4pfb_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip4pfb_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip4pfb_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip4pfb_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip4pfb_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip4pfb_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip4pfb_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip4pfb_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip4pfb_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip4pfb_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip4pfb_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip4pfb_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip4pfb_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip4pfb_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip4pfb_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip4pfb_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip4pfb_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip4pfb_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip4pfb_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip4pfb_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip4pfb_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip4pfb_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip4pfb_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip4pfb_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip4pfb_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip4pfb_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip4pfb_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip4pfb_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip4pfb_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip4pfb_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip4pfb_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip4pfb_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip4pfb_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip4pfb_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip4pfb_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip4pfb_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip4pfb_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip4pfb_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip4pfb_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip4pfb_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip4pfb_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip4pfb_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip4pfb_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip4pfb_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip4pfb_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip4pfb_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip4pfb_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip4pfb_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip4pfb_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip4pfb_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip4pfb_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip4pfb_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip4pfb_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip4pfb_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip4pfb_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip4p-fb-O" charge="0"/>
<Atom name="H1" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="H2" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="M" type="tip4p-fb-M" charge="-1.0517362213526e+00"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="8.203146574531e-01" weight2="8.984267127345e-02" weight3="8.984267127345e-02"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip4p-fb-O" type2="tip4p-fb-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip4p-fb-H" type2="tip4p-fb-O" type3="tip4p-fb-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.4350874656" sigma="0.14396923285147886" type="tip4pfb_standard-Li+"/>
<Atom epsilon="0.7047424999999999" sigma="0.21844836568801118" type="tip4pfb_standard-Na+"/>
<Atom epsilon="1.1692819784000001" sigma="0.2833057923686279" type="tip4pfb_standard-K+"/>
<Atom epsilon="1.8122970896000001" sigma="0.304509181860368" type="tip4pfb_standard-Rb+"/>
<Atom epsilon="1.6503026512" sigma="0.3364033559697921" type="tip4pfb_standard-Cs+"/>
<Atom epsilon="0.0065906368" sigma="0.4522201893280362" type="tip4pfb_standard-F-"/>
<Atom epsilon="0.048791716" sigma="0.49177609241346726" type="tip4pfb_standard-Cl-"/>
<Atom epsilon="0.1270986232" sigma="0.4932015303624918" type="tip4pfb_standard-Br-"/>
<Atom epsilon="0.1745071088" sigma="0.5259866031900563" type="tip4pfb_standard-I-"/>
<Atom epsilon="4.853439999999999e-06" sigma="0.1635690046505663" type="tip4pfb_standard-Be2+"/>
<Atom epsilon="0.00424537928" sigma="0.2129247936355411" type="tip4pfb_standard-Cu2+"/>
<Atom epsilon="0.00651925776" sigma="0.21755746696987088" type="tip4pfb_standard-Ni2+"/>
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="tip4pfb_standard-Pt2+"/>
<Atom epsilon="0.01050071032" sigma="0.22308103902234097" type="tip4pfb_standard-Zn2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Co2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Pd2+"/>
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="tip4pfb_standard-Ag2+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr2+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="tip4pfb_standard-Fe2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-Mg2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-V2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Mn2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Hg2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="tip4pfb_standard-Cd2+"/>
<Atom epsilon="0.45559312408" sigma="0.29470929596082424" type="tip4pfb_standard-Yb2+"/>
<Atom epsilon="0.46311578872000003" sigma="0.29524383519170844" type="tip4pfb_standard-Ca2+"/>
<Atom epsilon="0.49648724720000004" sigma="0.29756017185887335" type="tip4pfb_standard-Sn2+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip4pfb_standard-Pb2+"/>
<Atom epsilon="0.9712365224" sigma="0.3248216726339677" type="tip4pfb_standard-Eu2+"/>
<Atom epsilon="0.985288068" sigma="0.32553439160847997" type="tip4pfb_standard-Sr2+"/>
<Atom epsilon="1.02424478992" sigma="0.3274943687883887" type="tip4pfb_standard-Sm2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ba2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ra2+"/>
<Atom epsilon="0.01678206584" sigma="0.22896097056206718" type="tip4pfb_standard-Al3+"/>
<Atom epsilon="0.05043699032" sigma="0.2449971474885933" type="tip4pfb_standard-Fe3+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr3+"/>
<Atom epsilon="0.10650049832000001" sigma="0.2583606282606984" type="tip4pfb_standard-In3+"/>
<Atom epsilon="0.16579982824" sigma="0.2676259749293579" type="tip4pfb_standard-Tl3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Y3+"/>
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="tip4pfb_standard-La3+"/>
<Atom epsilon="0.66295839824" sigma="0.3080727767329294" type="tip4pfb_standard-Ce3+"/>
<Atom epsilon="0.64198735344" sigma="0.30682551852753287" type="tip4pfb_standard-Pr3+"/>
<Atom epsilon="0.49387597096" sigma="0.2973819921152453" type="tip4pfb_standard-Nd3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip4pfb_standard-Sm3+"/>
<Atom epsilon="0.4580931896" sigma="0.29488747570445234" type="tip4pfb_standard-Eu3+"/>
<Atom epsilon="0.35748949536" sigma="0.2872257467284454" type="tip4pfb_standard-Gd3+"/>
<Atom epsilon="0.37289213824" sigma="0.28847300493384187" type="tip4pfb_standard-Tb3+"/>
<Atom epsilon="0.32577870832" sigma="0.28455305057402436" type="tip4pfb_standard-Dy3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Er3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Tm3+"/>
<Atom epsilon="0.28625681168" sigma="0.280989455701463" type="tip4pfb_standard-Lu3+"/>
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="tip4pfb_standard-Hf4+"/>
<Atom epsilon="0.16712607256" sigma="0.26780415467298596" type="tip4pfb_standard-Zr4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-Ce4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-U4+"/>
<Atom epsilon="0.43343181496" sigma="0.29310567826817163" type="tip4pfb_standard-Pu4+"/>
<Atom epsilon="0.5502288444000001" sigma="0.3011237667314347" type="tip4pfb_standard-Th4+"/>
<Atom type="tip4p-fb-O" sigma="3.165552430462e-01" epsilon="7.492790213533e-01"/>
<Atom type="tip4p-fb-H" sigma="1" epsilon="0"/>
<Atom type="tip4p-fb-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/simtk/openmm/app/data/charmm36.xml 0 → 100644
View file @ 65920c60
This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/simtk/openmm/app/data/charmm36/spce.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_spc.str" md5hash="0d8c56cbaa3d3fa6fd0352e11826c12d" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_spc.str</Source>
<Reference Reference="H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331" forcefield="spc">H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
</AtomTypes>
<Residues>
<Residue name="SPC">
<Atom charge="-0.8068" name="OH2" type="OT"/>
<Atom charge="0.4034" name="H1" type="HT"/>
<Atom charge="0.4034" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR"/>
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond k="0.0" length="0.1633" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.1" type1="HT" type2="OT"/>
<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.9106119321581925" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
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<Atom epsilon="0.0" sigma="1.0" type="OT"/>
<Atom epsilon="0.0" sigma="1.0" type="OX"/>
<Atom epsilon="0.0" sigma="1.0" type="LIT"/>
<Atom epsilon="0.0" sigma="1.0" type="SOD"/>
<Atom epsilon="0.0" sigma="1.0" type="MG"/>
<Atom epsilon="0.0" sigma="1.0" type="POT"/>
<Atom epsilon="0.0" sigma="1.0" type="CAL"/>
<Atom epsilon="0.0" sigma="1.0" type="RUB"/>
<Atom epsilon="0.0" sigma="1.0" type="CES"/>
<Atom epsilon="0.0" sigma="1.0" type="BAR"/>
<Atom epsilon="0.0" sigma="1.0" type="ZN"/>
<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom epsilon="4.184e-06" sigma="1.7817974362806786e-05" type="HT"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.64973336" sigma="0.31410006292063597" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
<Atom epsilon="0.50208" sigma="0.24357170953956878" type="CAL"/>
<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
<Atom epsilon="0.79496" sigma="0.37417746161894255" type="CES"/>
<Atom epsilon="0.6276" sigma="0.33675971545704825" type="BAR"/>
<Atom epsilon="1.046" sigma="0.194215920554594" type="ZN"/>
<Atom epsilon="0.50208" sigma="0.2417899121032881" type="CAD"/>
<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/tip3p-pme-b.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str" md5hash="52fc5f1cff9a0a88ea24adf588612a54" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str</Source>
<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-b">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
</AtomTypes>
<Residues>
<Residue name="TP3B">
<Atom charge="-0.83" name="OH2" type="OT"/>
<Atom charge="0.415" name="H1" type="HT"/>
<Atom charge="0.415" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR"/>
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond k="0.0" length="0.15139000000000002" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.09572000000000001" type1="HT" type2="OT"/>
<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
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<Atom epsilon="0.0" sigma="1.0" type="OT"/>
<Atom epsilon="0.0" sigma="1.0" type="OX"/>
<Atom epsilon="0.0" sigma="1.0" type="LIT"/>
<Atom epsilon="0.0" sigma="1.0" type="SOD"/>
<Atom epsilon="0.0" sigma="1.0" type="MG"/>
<Atom epsilon="0.0" sigma="1.0" type="POT"/>
<Atom epsilon="0.0" sigma="1.0" type="CAL"/>
<Atom epsilon="0.0" sigma="1.0" type="RUB"/>
<Atom epsilon="0.0" sigma="1.0" type="CES"/>
<Atom epsilon="0.0" sigma="1.0" type="BAR"/>
<Atom epsilon="0.0" sigma="1.0" type="ZN"/>
<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.426768" sigma="0.31879919729933903" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
<Atom epsilon="0.50208" sigma="0.24357170953956878" type="CAL"/>
<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
<Atom epsilon="0.79496" sigma="0.37417746161894255" type="CES"/>
<Atom epsilon="0.6276" sigma="0.33675971545704825" type="BAR"/>
<Atom epsilon="1.046" sigma="0.194215920554594" type="ZN"/>
<Atom epsilon="0.50208" sigma="0.2417899121032881" type="CAD"/>
<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
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