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Commit 94e0853a authored by Evan Pretti's avatar Evan Pretti
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Copy water models from Amber14 to Amber 19 and update paths

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docs-source/usersguide/application/02_running_sims.rst
View file @ 94e0853a
......@@ -25,7 +25,7 @@ steps.
from sys import stdout
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
......@@ -87,14 +87,14 @@ 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`.
::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
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 :numref:`force-fields`).
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 :numref:`creating-force-fields`.
In this case we load two of those files: :file:`amber19-all.xml`, which contains the
Amber19 force field, and :file:`amber14/tip3pfb.xml`, which contains the TIP3P-FB water model. The
Amber19 force field, and :file:`amber19/tip3pfb.xml`, which contains the TIP3P-FB water model. The
:class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
::
......@@ -456,7 +456,7 @@ the main force field, and possibly a second file to define the water model
(either implicit or explicit). For example:
::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
In some cases, one XML file may load several others. For example, :file:`amber19-all.xml`
is really just a shortcut for loading several different files that together make up
......@@ -488,29 +488,29 @@ File Parameters
:file:`amber19/DNA.OL21.xml` DNA\ :cite:`Zgarbova2021`
:file:`amber14/RNA.OL3.xml` RNA
:file:`amber14/GLYCAM_06j-1.xml` Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007`
: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
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
:file:`amber19/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions
:file:`amber19/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions
:file:`amber19/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber19/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber19/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:file:`amber19/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:file:`amber19/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ===========================================
As a convenience, the file :file:`amber19-all.xml` can be used as a shortcut to
include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`, and
:file:`amber14/RNA.OL3.xml`. In most cases, you can simply include that file,
plus one of the water models, such as :file:`amber14/tip3pfb.xml` for the
plus one of the water models, such as :file:`amber19/tip3pfb.xml` for the
TIP3P-FB water model and ions\ :cite:`Wang2014`:
::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
GLYCAM is not included by default, since it is quite large. If your system contains
carbohydrates, include that file as well:
::
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml', 'amber19/GLYCAM_06j-1.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml', 'amber14/GLYCAM_06j-1.xml')
Be aware that GLYCAM works somewhat differently from most force fields. It uses
its own nonstandard `naming convention <https://glycam.org/docs/forcefield/glycam-naming-2/index.html>`_
......@@ -524,9 +524,9 @@ to them.
the Amber14 and Amber19 force fields and can be used with the files in the
:code:`amber19` directory.
.. tip:: The solvent model XML files included under the :file:`amber14/` directory
.. tip:: The solvent model XML files included under the :file:`amber19/` directory
include both water *and* ions compatible with that water model, so if you
mistakenly specify :file:`tip3p.xml` instead of :file:`amber14/tip3p.xml`,
mistakenly specify :file:`tip3p.xml` instead of :file:`amber19/tip3p.xml`,
you run the risk of having :class:`ForceField` throw an exception since
:file:`tip3p.xml` will be missing parameters for ions in your system.
......@@ -569,10 +569,15 @@ File Parameters
: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
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
:file:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:file:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ============================================
.. tip::
The XML files for water and ions provided in the :file:`amber14/` directory
are identical to those in the :file:`amber19/` directory. They are provided
in both directories for compatibility and convenience.
The converted parameter sets come from the `AmberTools 17 release <http://ambermd.org/AmberTools.php>`_
and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
......
examples/simulatePdb.py
View file @ 94e0853a
......@@ -4,7 +4,7 @@ from openmm.unit import *
from sys import stdout
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml')
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
......
wrappers/python/openmm/app/data/amber19/opc.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/opc3.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/spce.xml 0 → 100644
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<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+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="spce_standard-Ni2+"/>
</Residue>
<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+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="spce_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="spce_standard-Pr3+"/>
</Residue>
<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+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="spce_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="spce_standard-Sm3+"/>
</Residue>
<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+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="spce_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="spce_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="spce_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="spce_standard-Tl3+"/>
</Residue>
<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/openmm/app/data/amber19/tip3p.xml 0 → 100644
View file @ 94e0853a
<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/openmm/app/data/amber19/tip3pfb.xml 0 → 100644
View file @ 94e0853a
<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/openmm/app/data/amber19/tip4pew.xml 0 → 100644
View file @ 94e0853a
<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/openmm/app/data/amber19/tip4pfb.xml 0 → 100644
View file @ 94e0853a
<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
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