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Merge pull request #4916 from epretti/update-charmm-amber-ffs 

Add new CHARMM and Amber force fields
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docs-source/usersguide/application/02_running_sims.rst
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...@@ -11,7 +11,7 @@ A First Example ...@@ -11,7 +11,7 @@ A First Example
*************** ***************
Let’s begin with our first example of an OpenMM script. It loads a PDB file Let’s begin with our first example of an OpenMM script. It loads a PDB file
called :file:`input.pdb` that defines a biomolecular system, parameterizes it using the Amber14 force field and TIP3P-FB water called :file:`input.pdb` that defines a biomolecular system, parameterizes it using the Amber19 force field and TIP3P-FB water
model, energy minimizes it, simulates it for 10,000 steps with a Langevin model, energy minimizes it, simulates it for 10,000 steps with a Langevin
integrator, and saves a snapshot frame to a DCD file called :file:`output.dcd` every 1000 time integrator, and saves a snapshot frame to a DCD file called :file:`output.dcd` every 1000 time
steps. steps.
...@@ -25,7 +25,7 @@ steps. ...@@ -25,7 +25,7 @@ steps.
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=1*nanometer, constraints=HBonds) nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds) 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 ...@@ -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`. files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`.
:: ::
forcefield = ForceField('amber14-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 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`). 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, 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`. 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:`amber14-all.xml`, which contains the In this case we load two of those files: :file:`amber19-all.xml`, which contains the
Amber14 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`\ . :class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
:: ::
...@@ -456,11 +456,11 @@ the main force field, and possibly a second file to define the water model ...@@ -456,11 +456,11 @@ the main force field, and possibly a second file to define the water model
(either implicit or explicit). For example: (either implicit or explicit). For example:
:: ::
forcefield = ForceField('amber14-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:`amber14-all.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 is really just a shortcut for loading several different files that together make up
the AMBER14 force field. If you need finer grained control over which parameters the Amber19 force field. If you need finer grained control over which parameters
are loaded, you can instead specify the component files individually. are loaded, you can instead specify the component files individually.
Be aware that some force fields and water models include "extra particles", such Be aware that some force fields and water models include "extra particles", such
...@@ -472,47 +472,45 @@ must first add the extra particles to the :class:`Topology`. See section ...@@ -472,47 +472,45 @@ must first add the extra particles to the :class:`Topology`. See section
The force fields described below are the ones that are bundled with OpenMM. The force fields described below are the ones that are bundled with OpenMM.
Additional force fields are available online at https://github.com/openmm/openmmforcefields. Additional force fields are available online at https://github.com/openmm/openmmforcefields.
Amber14 Amber19
------- -------
The Amber14\ :cite:`Maier2015` force field is made up of various files that define The Amber19 force field is made up of various files that define parameters for
parameters for proteins, DNA, RNA, lipids, water, and ions. proteins, DNA, RNA, water, and ions.
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
=================================== ============================================ =================================== ===========================================
File Parameters File Parameters
=================================== ============================================ =================================== ===========================================
:file:`amber14/protein.ff14SB.xml` Protein (recommended) :file:`amber19/protein.ff19SB.xml` Protein\ :cite:`Tian2020` (recommended, includes residue-specific CMAP terms)
:file:`amber14/protein.ff15ipq.xml` Protein (alternative) :file:`amber19/protein.ff19ipq.xml` Protein (alternative)
:file:`amber14/DNA.OL15.xml` DNA (recommended) :file:`amber19/DNA.OL21.xml` DNA\ :cite:`Zgarbova2021`
:file:`amber14/DNA.bsc1.xml` DNA (alternative)
:file:`amber14/RNA.OL3.xml` RNA :file:`amber14/RNA.OL3.xml` RNA
:file:`amber14/lipid17.xml` Lipid
:file:`amber14/GLYCAM_06j-1.xml` Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007` :file:`amber14/GLYCAM_06j-1.xml` Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007`
:file:`amber14/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions :file:`amber19/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions
:file:`amber14/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions :file:`amber19/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions :file:`amber19/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions :file:`amber19/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`amber19/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions :file:`amber19/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions :file:`amber19/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ============================================ =================================== ===========================================
As a convenience, the file :file:`amber14-all.xml` can be used as a shortcut to include As a convenience, the file :file:`amber19-all.xml` can be used as a shortcut to
:file:`amber14/protein.ff14SB.xml`, :file:`amber14/DNA.OL15.xml`, :file:`amber14/RNA.OL3.xml`, include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`, and
and :file:`amber14/lipid17.xml`. In most cases, you can simply include that file, :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 TIP3P-FB plus one of the water models, such as :file:`amber19/tip3pfb.xml` for the
water model and ions\ :cite:`Wang2014`: TIP3P-FB water model and ions\ :cite:`Wang2014`:
:: ::
forcefield = ForceField('amber14-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 GLYCAM is not included by default, since it is quite large. If your system contains
carbohydrates, include that file as well: carbohydrates, include that file as well:
:: ::
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml', 'amber14/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 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>`_ its own nonstandard `naming convention <https://glycam.org/docs/forcefield/glycam-naming-2/index.html>`_
...@@ -520,14 +518,68 @@ for carbohydrates, and requires your input file to follow it. If any residues h ...@@ -520,14 +518,68 @@ for carbohydrates, and requires your input file to follow it. If any residues h
names different from what it expects, GLYCAM will be unable to assign parameters names different from what it expects, GLYCAM will be unable to assign parameters
to them. to them.
.. tip:: The solvent model XML files included under the :file:`amber14/` directory .. tip::
Files in the :code:`amber14` directory are used by the older Amber14 force
field described below, but those also listed in the table above are shared between
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:`amber19/` directory
include both water *and* ions compatible with that water model, so if you 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 you run the risk of having :class:`ForceField` throw an exception since
:file:`tip3p.xml` will be missing parameters for ions in your system. :file:`tip3p.xml` will be missing parameters for ions in your system.
.. warning::
The updated Lipid21 lipid force field is not yet supported in this port of
Amber19, as it makes use of Amber features not yet supported in
`ParmEd <https://github.com/parmed/parmed>`_. Amber19 should be preferred
over Amber14 for simulations not requiring a lipid force field, but Amber14
should be used if the Lipid17 force field is desired. Alternatively, to use
Amber19 with Lipid21, you can prepare your system with AmberTools_ before
loading it into OpenMM, as described in Section :numref:`using_amber_files`.
The converted parameter sets come from the `AmberTools 24 release <http://ambermd.org/AmberTools.php>`_
and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
Amber14
-------
Similarly to the Amber19 force field, Amber14\ :cite:`Maier2015` is made up of
various files that define parameters for proteins, DNA, RNA, lipids, water, and
ions. The file :file:`amber14-all.xml` can be used as a shortcut to include
:file:`amber14/protein.ff14SB.xml`, :file:`amber14/DNA.OL15.xml`,
:file:`amber14/RNA.OL3.xml`, and :file:`amber14/lipid17.xml`. The same remarks
for Amber19 regarding water, ions, and GLYCAM apply to Amber14.
.. tabularcolumns:: |l|L|
=================================== ============================================
File Parameters
=================================== ============================================
:file:`amber14/protein.ff14SB.xml` Protein (recommended)
:file:`amber14/protein.ff15ipq.xml` Protein (alternative)
:file:`amber14/DNA.OL15.xml` DNA (recommended)
:file:`amber14/DNA.bsc1.xml` DNA (alternative)
:file:`amber14/RNA.OL3.xml` RNA
:file:`amber14/lipid17.xml` Lipid
:file:`amber14/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
: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>`_ The converted parameter sets come from the `AmberTools 17 release <http://ambermd.org/AmberTools.php>`_
and were converted using the `openmmforcefields <https://github.com/openmm/openmmforcefields>`_ package and `ParmEd <https://github.com/parmed/parmed>`_. and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
CHARMM36 CHARMM36
-------- --------
...@@ -541,7 +593,7 @@ for full references). ...@@ -541,7 +593,7 @@ for full references).
================================= ============================================ ================================= ============================================
File Parameters File Parameters
================================= ============================================ ================================= ============================================
:file:`charmm36.xml` Protein, DNA, RNA, lipids, carbohydrates, and small molecules :file:`charmm36_2024.xml` Protein, DNA, RNA, lipids, carbohydrates, and small molecules
:file:`charmm36/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions :file:`charmm36/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions
:file:`charmm36/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`charmm36/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:file:`charmm36/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions :file:`charmm36/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions
...@@ -552,19 +604,13 @@ File Parameters ...@@ -552,19 +604,13 @@ File Parameters
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions :file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
================================= ============================================ ================================= ============================================
The file :file:`charmm36.xml` bundles everything but the water and ions into a single The file :file:`charmm36_2024.xml` bundles everything but the water and ions into a single
file. In most cases, you can simply include that file, plus one of the water models, file. In most cases, you can simply include that file, plus one of the water models,
such as :file:`charmm36/water.xml`, which specifies the default CHARMM water model such as :file:`charmm36/water.xml`, which specifies the default CHARMM water model
(a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions: (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions:
:: ::
forcefield = ForceField('charmm36.xml', 'charmm36/water.xml') forcefield = ForceField('charmm36_2024.xml', 'charmm36/water.xml')
.. warning:: Drude polarizable sites and lone pairs are not yet supported
by `ParmEd <https://github.com/parmed/parmed>`_ and the CHARMM36 forcefields
that depend on these features are not included in this port.
To use the CHARMM 2019 polarizable force field\ :cite:`Lopes2013`,
include the single file :file:`charmm_polar_2019.xml`.
.. tip:: The solvent model XML files included under the :file:`charmm36/` directory .. tip:: The solvent model XML files included under the :file:`charmm36/` directory
include both water *and* ions compatible with that water model, so if you include both water *and* ions compatible with that water model, so if you
...@@ -595,8 +641,18 @@ such as :file:`charmm36/water.xml`, which specifies the default CHARMM water mod ...@@ -595,8 +641,18 @@ such as :file:`charmm36/water.xml`, which specifies the default CHARMM water mod
`CHARMM-GUI <http://charmm-gui.org/>`_, it's easiest to load `CHARMM-GUI <http://charmm-gui.org/>`_, it's easiest to load
the PSF file directly, as discussed in Section :numref:`using-charmm-files`. the PSF file directly, as discussed in Section :numref:`using-charmm-files`.
The converted parameter sets come from the `CHARMM36 July 2017 update <http://mackerell.umaryland.edu/charmm_ff.shtml>`_ .. warning:: Some residues and patches are not included in this port of
and were converted using the `openmmforcefields <https://github.com/openmm/openmmforcefields>`_ package and `parmed <https://github.com/parmed/parmed>`_. CHARMM36, either due to a lack of support for certain CHARMM
features in `ParmEd <https://github.com/parmed/parmed>`_, or
because they generate a large number of residue-patch combinations,
slowing down parameterization. The openmmforcefields_ package
includes residues and patches not present in this port within
additional force field XML files that can be loaded as needed.
The converted parameter sets come from the
`CHARMM36 July 2024 update <http://mackerell.umaryland.edu/charmm_ff.shtml>`_,
which includes the CHARMM36m protein parameters. They were converted using the
openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
Implicit Solvent Implicit Solvent
---------------- ----------------
...@@ -606,7 +662,7 @@ Born implicit solvent models from AMBER. To use them, include an extra file whe ...@@ -606,7 +662,7 @@ Born implicit solvent models from AMBER. To use them, include an extra file whe
creating the ForceField. For example, creating the ForceField. For example,
:: ::
forcefield = ForceField('amber14-all.xml', 'implicit/gbn2.xml') forcefield = ForceField('amber19-all.xml', 'implicit/gbn2.xml')
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
...@@ -681,8 +737,8 @@ recommended for most simulations. ...@@ -681,8 +737,8 @@ recommended for most simulations.
CHARMM Polarizable Force Field CHARMM Polarizable Force Field
------------------------------ ------------------------------
To use the CHARMM 2019 polarizable force field\ :cite:`Lopes2013`, include the To use the CHARMM 2023 polarizable force field\ :cite:`Lopes2013`, include the
single file :file:`charmm_polar_2019.xml`. It includes parameters for proteins, lipids, single file :file:`charmm_polar_2023.xml`. It includes parameters for proteins, lipids, carbohydrates,
water, and ions. When using this force field, remember to add extra particles to water, and ions. When using this force field, remember to add extra particles to
the :class:`Topology` as described in section :numref:`adding-or-removing-extra-particles`. the :class:`Topology` as described in section :numref:`adding-or-removing-extra-particles`.
This force field also requires that you use one of the special integrators that This force field also requires that you use one of the special integrators that
...@@ -698,17 +754,19 @@ still useful for reproducing older results. ...@@ -698,17 +754,19 @@ still useful for reproducing older results.
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
============================= ================================================================================ ============================= ==================================================================================
File Force Field File Force Field
============================= ================================================================================ ============================= ==================================================================================
:code:`amber96.xml` Amber96\ :cite:`Kollman1997` :code:`amber96.xml` Amber96\ :cite:`Kollman1997`
:code:`amber99sb.xml` Amber99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006` :code:`amber99sb.xml` Amber99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
:code:`amber99sbildn.xml` Amber99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010` :code:`amber99sbildn.xml` Amber99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
:code:`amber99sbnmr.xml` Amber99SB with modifications to fit NMR data\ :cite:`Li2010` :code:`amber99sbnmr.xml` Amber99SB with modifications to fit NMR data\ :cite:`Li2010`
:code:`amber03.xml` Amber03\ :cite:`Duan2003` :code:`amber03.xml` Amber03\ :cite:`Duan2003`
:code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`) :code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`)
:code:`charmm36.xml` July 2017 release of the CHARMM36 force field without CHARMM36m protein parameters
:code:`charmm_polar_2013.xml` 2013 version of the CHARMM polarizable force field\ :cite:`Lopes2013` :code:`charmm_polar_2013.xml` 2013 version of the CHARMM polarizable force field\ :cite:`Lopes2013`
============================= ================================================================================ :code:`charmm_polar_2019.xml` 2019 version of the CHARMM polarizable force field\ :cite:`Lopes2013`
============================= ==================================================================================
Several of these force fields support implicit solvent. To enable it, also Several of these force fields support implicit solvent. To enable it, also
include the corresponding OBC file. include the corresponding OBC file.
...@@ -732,7 +790,7 @@ Water Models ...@@ -732,7 +790,7 @@ Water Models
------------ ------------
The following files define popular water models. They can be used with force fields The following files define popular water models. They can be used with force fields
that do not provide their own water models. When using Amber14 or CHARMM36, use that do not provide their own water models. When using Amber19, Amber14 or CHARMM36, use
the water files included with those force fields instead, since they also include the water files included with those force fields instead, since they also include
ion parameters. ion parameters.
......
docs-source/usersguide/conf.py
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...@@ -242,7 +242,7 @@ latex_elements = { ...@@ -242,7 +242,7 @@ latex_elements = {
\\captionsetup[figure]{labelformat=empty} \\captionsetup[figure]{labelformat=empty}
% Backwards compatibility for sphinx < 1.5 % Backwards compatibility for sphinx < 1.5
\\let\\DUspan\\null % force DUspan to be defined \\let\\DUspan\\null % force DUspan to be defined
\\renewcommand{\DUspan}[2]{% \\renewcommand{\\DUspan}[2]{%
\\IfEqCase{#1}{% \\IfEqCase{#1}{%
{code}{\\small{}\\texttt{#2}\\normalsize{}} {code}{\\small{}\\texttt{#2}\\normalsize{}}
}[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]% }[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]%
......
docs-source/usersguide/references.bib
View file @ 0f78d025
...@@ -717,3 +717,25 @@ ...@@ -717,3 +717,25 @@
doi = {10.1063/1.4960175}, doi = {10.1063/1.4960175},
type = {Journal Article} type = {Journal Article}
} }
@article{Tian2020,
title={ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution},
author={Tian, C. and Kasavajhala, K. and Belfon, K.A.A. and Raguette, L. and Huang, H. and Migues, A.N. and Bickel, J. and Wang, Y. and Pincay, J. and Wu, Q. and Simmerling, C.},
journal={Journal of Chemical Theory and Computation},
volume={16},
pages={528-552},
year={2020},
doi = {10.1021/acs.jctc.9b00591},
type = {Journal Article}
}
@article{Zgarbova2021,
title={Z-DNA as a touchstone for additive empirical force fields and a refinement of the alpha/gamma DNA torsions for AMBER},
author={Zgarbova, M. and Sponer, J. and Jurecka, P.},
journal={Journal of Chemical Theory and Computation},
volume={17},
pages={6292-6301},
year={2021},
doi = {10.1021/acs.jctc.1c00697},
type = {Journal Article}
}
examples/simulatePdb.py
View file @ 0f78d025
...@@ -4,7 +4,7 @@ from openmm.unit import * ...@@ -4,7 +4,7 @@ from openmm.unit import *
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber14-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) system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds) integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
simulation = Simulation(pdb.topology, system, integrator) simulation = Simulation(pdb.topology, system, integrator)
......
wrappers/python/openmm/app/data/amber14/GLYCAM_06j-1.xml
View file @ 0f78d025
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2021-10-29</DateGenerated> <DateGenerated>2025-04-30</DateGenerated>
<Source Source="glycam/leaprc.GLYCAM_06j-1" md5hash="a7359f8d717f92dba02d57d6e0c8f3f7" sourcePackage="AmberTools" sourcePackageVersion="20.15">glycam/leaprc.GLYCAM_06j-1</Source> <Source Source="glycam/leaprc.GLYCAM_06j-1" md5hash="a7359f8d717f92dba02d57d6e0c8f3f7" sourcePackage="AmberTools" sourcePackageVersion="24.8">glycam/leaprc.GLYCAM_06j-1</Source>
<Reference>R. Kadirvelraj; O. C. Grant; I. J. Goldstein; H. C. Winter; H. Tateno; E. Fadda; R. J. Woods. Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac&#945;2-6Gal&#946;1-4GlcNAc human- type influenza receptor. Glycobiology, 2011, 21, 973&#8211;984. M. L. DeMarco; R. J. Woods. From agonist to antagonist: Structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol. Immunol., 2011, 49, 124&#8211;133. B. L. Foley; M. B. Tessier; R. J. Woods. Carbohydrate force fields. WIREs Comput. Mol. Sci., 2012, 2, 652&#8211;697. E. Ficko-Blean; C. P. Stuart; M. D. Suits; M. Cid; M. Tessier; R. J. Woods; A. B. Boraston. Carbohy- drate Recognition by an Architecturally Complex &#945;-N-Acetylglucosaminidase from Clostridium perfrin- gens. PLoS ONE, 2012, 7, e33524.</Reference> <Reference>R. Kadirvelraj; O. C. Grant; I. J. Goldstein; H. C. Winter; H. Tateno; E. Fadda; R. J. Woods. Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac&#945;2-6Gal&#946;1-4GlcNAc human- type influenza receptor. Glycobiology, 2011, 21, 973&#8211;984. M. L. DeMarco; R. J. Woods. From agonist to antagonist: Structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol. Immunol., 2011, 49, 124&#8211;133. B. L. Foley; M. B. Tessier; R. J. Woods. Carbohydrate force fields. WIREs Comput. Mol. Sci., 2012, 2, 652&#8211;697. E. Ficko-Blean; C. P. Stuart; M. D. Suits; M. Cid; M. Tessier; R. J. Woods; A. B. Boraston. Carbohy- drate Recognition by an Architecturally Complex &#945;-N-Acetylglucosaminidase from Clostridium perfrin- gens. PLoS ONE, 2012, 7, e33524.</Reference>
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...@@ -342,8 +342,6 @@ ...@@ -342,8 +342,6 @@
<Bond atomName1="C2M" atomName2="H22" /> <Bond atomName1="C2M" atomName2="H22" />
<Bond atomName1="C2M" atomName2="H21" /> <Bond atomName1="C2M" atomName2="H21" />
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...@@ -1139,11 +1137,6 @@ ...@@ -1139,11 +1137,6 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
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...@@ -1841,9 +1834,6 @@ ...@@ -1841,9 +1834,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
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...@@ -1887,9 +1877,6 @@ ...@@ -1887,9 +1877,6 @@
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...@@ -2401,11 +2388,6 @@ ...@@ -2401,11 +2388,6 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
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...@@ -2483,11 +2465,6 @@ ...@@ -2483,11 +2465,6 @@
<Bond atomName1="C1" atomName2="O1B" /> <Bond atomName1="C1" atomName2="O1B" />
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<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
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<Atom name="C1" type="glycam-Cg" charge="0.456" /> <Atom name="C1" type="glycam-Cg" charge="0.456" />
...@@ -2711,9 +2688,6 @@ ...@@ -2711,9 +2688,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
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<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -2757,9 +2731,6 @@ ...@@ -2757,9 +2731,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
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<Residue name="0VA" override="1"> <Residue name="0VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -3313,9 +3284,6 @@ ...@@ -3313,9 +3284,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
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<Residue name="0ZB" override="1"> <Residue name="0ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -3359,9 +3327,6 @@ ...@@ -3359,9 +3327,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
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<Residue name="0aA" override="1"> <Residue name="0aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -3681,8 +3646,6 @@ ...@@ -3681,8 +3646,6 @@
<Bond atomName1="C2M" atomName2="H22" /> <Bond atomName1="C2M" atomName2="H22" />
<Bond atomName1="C2M" atomName2="H23" /> <Bond atomName1="C2M" atomName2="H23" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
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<Atom name="C2" type="glycam-Cg" charge="0.241" /> <Atom name="C2" type="glycam-Cg" charge="0.241" />
...@@ -4478,11 +4441,6 @@ ...@@ -4478,11 +4441,6 @@
<Bond atomName1="C1" atomName2="O1B" /> <Bond atomName1="C1" atomName2="O1B" />
<Bond atomName1="C1" atomName2="O1A" /> <Bond atomName1="C1" atomName2="O1A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
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<Atom name="C1" type="glycam-Cg" charge="0.394" /> <Atom name="C1" type="glycam-Cg" charge="0.394" />
...@@ -5180,9 +5138,6 @@ ...@@ -5180,9 +5138,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
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<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -5226,9 +5181,6 @@ ...@@ -5226,9 +5181,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
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<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -5740,11 +5692,6 @@ ...@@ -5740,11 +5692,6 @@
<Bond atomName1="C1" atomName2="O1B" /> <Bond atomName1="C1" atomName2="O1B" />
<Bond atomName1="C1" atomName2="O1A" /> <Bond atomName1="C1" atomName2="O1A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
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<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -5822,11 +5769,6 @@ ...@@ -5822,11 +5769,6 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
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<Atom name="C1" type="glycam-Cg" charge="0.456" /> <Atom name="C1" type="glycam-Cg" charge="0.456" />
...@@ -6050,9 +5992,6 @@ ...@@ -6050,9 +5992,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
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<ExternalBond atomName="O6B" />
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<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -6096,9 +6035,6 @@ ...@@ -6096,9 +6035,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="0vA" override="1"> <Residue name="0vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -6652,9 +6588,6 @@ ...@@ -6652,9 +6588,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
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<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -6698,9 +6631,6 @@ ...@@ -6698,9 +6631,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
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<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -8402,9 +8332,6 @@ ...@@ -8402,9 +8332,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
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<Residue name="1OB" override="1"> <Residue name="1OB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -8450,9 +8377,6 @@ ...@@ -8450,9 +8377,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
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<Residue name="1PA" override="1"> <Residue name="1PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -9128,9 +9052,6 @@ ...@@ -9128,9 +9052,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
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<Residue name="1UB" override="1"> <Residue name="1UB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -9176,9 +9097,6 @@ ...@@ -9176,9 +9097,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
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<Residue name="1VA" override="1"> <Residue name="1VA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -9754,9 +9672,6 @@ ...@@ -9754,9 +9672,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
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<Residue name="1ZB" override="1"> <Residue name="1ZB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -9802,9 +9717,6 @@ ...@@ -9802,9 +9717,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
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<Residue name="1aA" override="1"> <Residue name="1aA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -11506,9 +11418,6 @@ ...@@ -11506,9 +11418,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
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<Residue name="1oB" override="1"> <Residue name="1oB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -11554,9 +11463,6 @@ ...@@ -11554,9 +11463,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="1pA" override="1"> <Residue name="1pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -12232,9 +12138,6 @@ ...@@ -12232,9 +12138,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="1uB" override="1"> <Residue name="1uB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -12280,9 +12183,6 @@ ...@@ -12280,9 +12183,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="1vA" override="1"> <Residue name="1vA" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -12858,9 +12758,6 @@ ...@@ -12858,9 +12758,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="1zB" override="1"> <Residue name="1zB" override="1">
<Atom name="O1" type="glycam-Os" charge="-0.388" /> <Atom name="O1" type="glycam-Os" charge="-0.388" />
...@@ -12906,9 +12803,6 @@ ...@@ -12906,9 +12803,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="O1" /> <ExternalBond atomName="O1" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2AA" override="1"> <Residue name="2AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -14571,9 +14465,6 @@ ...@@ -14571,9 +14465,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2OB" override="1"> <Residue name="2OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -14616,9 +14507,6 @@ ...@@ -14616,9 +14507,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2PA" override="1"> <Residue name="2PA" override="1">
<Atom name="O2" type="glycam-Os" charge="-0.388" /> <Atom name="O2" type="glycam-Os" charge="-0.388" />
...@@ -15273,9 +15161,6 @@ ...@@ -15273,9 +15161,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2UB" override="1"> <Residue name="2UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -15318,9 +15203,6 @@ ...@@ -15318,9 +15203,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2XA" override="1"> <Residue name="2XA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.482" /> <Atom name="C1" type="glycam-Cg" charge="0.482" />
...@@ -15515,9 +15397,6 @@ ...@@ -15515,9 +15397,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2ZB" override="1"> <Residue name="2ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -15560,9 +15439,6 @@ ...@@ -15560,9 +15439,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2aA" override="1"> <Residue name="2aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -17225,9 +17101,6 @@ ...@@ -17225,9 +17101,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2oB" override="1"> <Residue name="2oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -17270,9 +17143,6 @@ ...@@ -17270,9 +17143,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2pA" override="1"> <Residue name="2pA" override="1">
<Atom name="O2" type="glycam-Os" charge="-0.388" /> <Atom name="O2" type="glycam-Os" charge="-0.388" />
...@@ -17927,9 +17797,6 @@ ...@@ -17927,9 +17797,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2uB" override="1"> <Residue name="2uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -17972,9 +17839,6 @@ ...@@ -17972,9 +17839,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="2xA" override="1"> <Residue name="2xA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.482" /> <Atom name="C1" type="glycam-Cg" charge="0.482" />
...@@ -18169,9 +18033,6 @@ ...@@ -18169,9 +18033,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="2zB" override="1"> <Residue name="2zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -18214,9 +18075,6 @@ ...@@ -18214,9 +18075,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3AA" override="1"> <Residue name="3AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -18529,8 +18387,6 @@ ...@@ -18529,8 +18387,6 @@
<Bond atomName1="C4M" atomName2="H41" /> <Bond atomName1="C4M" atomName2="H41" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue> </Residue>
<Residue name="3BD" override="1"> <Residue name="3BD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" /> <Atom name="C2" type="glycam-Cg" charge="0.241" />
...@@ -19913,9 +19769,6 @@ ...@@ -19913,9 +19769,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3OB" override="1"> <Residue name="3OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -19958,9 +19811,6 @@ ...@@ -19958,9 +19811,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3PA" override="1"> <Residue name="3PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -20519,9 +20369,6 @@ ...@@ -20519,9 +20369,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3UB" override="1"> <Residue name="3UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -20564,9 +20411,6 @@ ...@@ -20564,9 +20411,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3VA" override="1"> <Residue name="3VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -21109,9 +20953,6 @@ ...@@ -21109,9 +20953,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3ZB" override="1"> <Residue name="3ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -21154,9 +20995,6 @@ ...@@ -21154,9 +20995,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3aA" override="1"> <Residue name="3aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -21469,8 +21307,6 @@ ...@@ -21469,8 +21307,6 @@
<Bond atomName1="C2M" atomName2="H23" /> <Bond atomName1="C2M" atomName2="H23" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C4N" />
<ExternalBond atomName="O4N" />
</Residue> </Residue>
<Residue name="3bD" override="1"> <Residue name="3bD" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.241" /> <Atom name="C2" type="glycam-Cg" charge="0.241" />
...@@ -22853,9 +22689,6 @@ ...@@ -22853,9 +22689,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3oB" override="1"> <Residue name="3oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -22898,9 +22731,6 @@ ...@@ -22898,9 +22731,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3pA" override="1"> <Residue name="3pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -23459,9 +23289,6 @@ ...@@ -23459,9 +23289,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3uB" override="1"> <Residue name="3uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -23504,9 +23331,6 @@ ...@@ -23504,9 +23331,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="3vA" override="1"> <Residue name="3vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -24049,9 +23873,6 @@ ...@@ -24049,9 +23873,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="3zB" override="1"> <Residue name="3zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -24094,9 +23915,6 @@ ...@@ -24094,9 +23915,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4AA" override="1"> <Residue name="4AA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -24967,11 +24785,6 @@ ...@@ -24967,11 +24785,6 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4HA" override="1"> <Residue name="4HA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" /> <Atom name="C1" type="glycam-Cg" charge="0.394" />
...@@ -25654,9 +25467,6 @@ ...@@ -25654,9 +25467,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4OB" override="1"> <Residue name="4OB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -25699,9 +25509,6 @@ ...@@ -25699,9 +25509,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4PA" override="1"> <Residue name="4PA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -26126,11 +25933,6 @@ ...@@ -26126,11 +25933,6 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4SB" override="1"> <Residue name="4SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -26207,11 +26009,6 @@ ...@@ -26207,11 +26009,6 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4TA" override="1"> <Residue name="4TA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" /> <Atom name="C1" type="glycam-Cg" charge="0.456" />
...@@ -26430,9 +26227,6 @@ ...@@ -26430,9 +26227,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4UB" override="1"> <Residue name="4UB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -26475,9 +26269,6 @@ ...@@ -26475,9 +26269,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4VA" override="1"> <Residue name="4VA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -26944,9 +26735,6 @@ ...@@ -26944,9 +26735,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4ZB" override="1"> <Residue name="4ZB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -26989,9 +26777,6 @@ ...@@ -26989,9 +26777,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4aA" override="1"> <Residue name="4aA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.448" /> <Atom name="C1" type="glycam-Cg" charge="0.448" />
...@@ -27862,11 +27647,6 @@ ...@@ -27862,11 +27647,6 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4hA" override="1"> <Residue name="4hA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.394" /> <Atom name="C1" type="glycam-Cg" charge="0.394" />
...@@ -28549,9 +28329,6 @@ ...@@ -28549,9 +28329,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4oB" override="1"> <Residue name="4oB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.301" /> <Atom name="C1" type="glycam-Cg" charge="0.301" />
...@@ -28594,9 +28371,6 @@ ...@@ -28594,9 +28371,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4pA" override="1"> <Residue name="4pA" override="1">
<Atom name="C2" type="glycam-Cg" charge="0.417" /> <Atom name="C2" type="glycam-Cg" charge="0.417" />
...@@ -29021,11 +28795,6 @@ ...@@ -29021,11 +28795,6 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4sB" override="1"> <Residue name="4sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -29102,11 +28871,6 @@ ...@@ -29102,11 +28871,6 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="4tA" override="1"> <Residue name="4tA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.456" /> <Atom name="C1" type="glycam-Cg" charge="0.456" />
...@@ -29325,9 +29089,6 @@ ...@@ -29325,9 +29089,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4uB" override="1"> <Residue name="4uB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.278" /> <Atom name="C1" type="glycam-Cg" charge="0.278" />
...@@ -29370,9 +29131,6 @@ ...@@ -29370,9 +29131,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="4vA" override="1"> <Residue name="4vA" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.389" /> <Atom name="C1" type="glycam-Cg" charge="0.389" />
...@@ -29839,9 +29597,6 @@ ...@@ -29839,9 +29597,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
</Residue> </Residue>
<Residue name="4zB" override="1"> <Residue name="4zB" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.251" /> <Atom name="C1" type="glycam-Cg" charge="0.251" />
...@@ -29884,9 +29639,6 @@ ...@@ -29884,9 +29639,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
</Residue> </Residue>
<Residue name="5AD" override="1"> <Residue name="5AD" override="1">
<Atom name="C1" type="glycam-Cg" charge="0.368" /> <Atom name="C1" type="glycam-Cg" charge="0.368" />
...@@ -34029,11 +33781,6 @@ ...@@ -34029,11 +33781,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="7SA" override="1"> <Residue name="7SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -34110,11 +33857,6 @@ ...@@ -34110,11 +33857,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="7SB" override="1"> <Residue name="7SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -34191,11 +33933,6 @@ ...@@ -34191,11 +33933,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="7gL" override="1"> <Residue name="7gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -34274,11 +34011,6 @@ ...@@ -34274,11 +34011,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="7sA" override="1"> <Residue name="7sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -34355,11 +34087,6 @@ ...@@ -34355,11 +34087,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="7sB" override="1"> <Residue name="7sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -34436,11 +34163,6 @@ ...@@ -34436,11 +34163,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8GL" override="1"> <Residue name="8GL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -34519,11 +34241,6 @@ ...@@ -34519,11 +34241,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8SA" override="1"> <Residue name="8SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -34600,11 +34317,6 @@ ...@@ -34600,11 +34317,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8SB" override="1"> <Residue name="8SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -34681,11 +34393,6 @@ ...@@ -34681,11 +34393,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8gL" override="1"> <Residue name="8gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -34764,11 +34471,6 @@ ...@@ -34764,11 +34471,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8sA" override="1"> <Residue name="8sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -34845,11 +34547,6 @@ ...@@ -34845,11 +34547,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="8sB" override="1"> <Residue name="8sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -34926,11 +34623,6 @@ ...@@ -34926,11 +34623,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9GL" override="1"> <Residue name="9GL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -35009,11 +34701,6 @@ ...@@ -35009,11 +34701,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9SA" override="1"> <Residue name="9SA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -35090,11 +34777,6 @@ ...@@ -35090,11 +34777,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9SB" override="1"> <Residue name="9SB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -35171,11 +34853,6 @@ ...@@ -35171,11 +34853,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9gL" override="1"> <Residue name="9gL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -35254,11 +34931,6 @@ ...@@ -35254,11 +34931,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9sA" override="1"> <Residue name="9sA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -35335,11 +35007,6 @@ ...@@ -35335,11 +35007,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="9sB" override="1"> <Residue name="9sB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -35416,11 +35083,6 @@ ...@@ -35416,11 +35083,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ACX" override="1"> <Residue name="ACX" override="1">
<Atom name="C1A" type="protein-C" charge="0.763" /> <Atom name="C1A" type="protein-C" charge="0.763" />
...@@ -35435,7 +35097,6 @@ ...@@ -35435,7 +35097,6 @@
<Bond atomName1="C2A" atomName2="H2A" /> <Bond atomName1="C2A" atomName2="H2A" />
<Bond atomName1="C2A" atomName2="H3A" /> <Bond atomName1="C2A" atomName2="H3A" />
<ExternalBond atomName="C1A" /> <ExternalBond atomName="C1A" />
<ExternalBond atomName="O1A" />
</Residue> </Residue>
<Residue name="AGL" override="1"> <Residue name="AGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -35508,14 +35169,9 @@ ...@@ -35508,14 +35169,9 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ASA" override="1"> <Residue name="ASA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -35586,14 +35242,9 @@ ...@@ -35586,14 +35242,9 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ASB" override="1"> <Residue name="ASB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -35664,14 +35315,9 @@ ...@@ -35664,14 +35315,9 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="AgL" override="1"> <Residue name="AgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -35744,14 +35390,9 @@ ...@@ -35744,14 +35390,9 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="AsA" override="1"> <Residue name="AsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -35822,14 +35463,9 @@ ...@@ -35822,14 +35463,9 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="AsB" override="1"> <Residue name="AsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -35900,14 +35536,9 @@ ...@@ -35900,14 +35536,9 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="BGL" override="1"> <Residue name="BGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -35982,11 +35613,6 @@ ...@@ -35982,11 +35613,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
...@@ -36061,11 +35687,6 @@ ...@@ -36061,11 +35687,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
...@@ -36140,11 +35761,6 @@ ...@@ -36140,11 +35761,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
...@@ -36221,11 +35837,6 @@ ...@@ -36221,11 +35837,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
...@@ -36300,11 +35911,6 @@ ...@@ -36300,11 +35911,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
...@@ -36379,11 +35985,6 @@ ...@@ -36379,11 +35985,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
...@@ -36460,13 +36061,8 @@ ...@@ -36460,13 +36061,8 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="CSA" override="1"> <Residue name="CSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -36539,13 +36135,8 @@ ...@@ -36539,13 +36135,8 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="CSB" override="1"> <Residue name="CSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -36618,13 +36209,8 @@ ...@@ -36618,13 +36209,8 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="CgL" override="1"> <Residue name="CgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -36699,13 +36285,8 @@ ...@@ -36699,13 +36285,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="CsA" override="1"> <Residue name="CsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -36778,13 +36359,8 @@ ...@@ -36778,13 +36359,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="CsB" override="1"> <Residue name="CsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -36857,13 +36433,8 @@ ...@@ -36857,13 +36433,8 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DGL" override="1"> <Residue name="DGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -36938,13 +36509,8 @@ ...@@ -36938,13 +36509,8 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DSA" override="1"> <Residue name="DSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -37017,13 +36583,8 @@ ...@@ -37017,13 +36583,8 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DSB" override="1"> <Residue name="DSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -37096,13 +36657,8 @@ ...@@ -37096,13 +36657,8 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DgL" override="1"> <Residue name="DgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -37177,13 +36733,8 @@ ...@@ -37177,13 +36733,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DsA" override="1"> <Residue name="DsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -37256,13 +36807,8 @@ ...@@ -37256,13 +36807,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="DsB" override="1"> <Residue name="DsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -37335,13 +36881,8 @@ ...@@ -37335,13 +36881,8 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="EGL" override="1"> <Residue name="EGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -37416,13 +36957,8 @@ ...@@ -37416,13 +36957,8 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ESA" override="1"> <Residue name="ESA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -37495,13 +37031,8 @@ ...@@ -37495,13 +37031,8 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ESB" override="1"> <Residue name="ESB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -37574,13 +37105,8 @@ ...@@ -37574,13 +37105,8 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="EgL" override="1"> <Residue name="EgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -37655,13 +37181,8 @@ ...@@ -37655,13 +37181,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="EsA" override="1"> <Residue name="EsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -37734,13 +37255,8 @@ ...@@ -37734,13 +37255,8 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="EsB" override="1"> <Residue name="EsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -37813,13 +37329,8 @@ ...@@ -37813,13 +37329,8 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="FGL" override="1"> <Residue name="FGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -37896,11 +37407,6 @@ ...@@ -37896,11 +37407,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="FSA" override="1"> <Residue name="FSA" override="1">
...@@ -37976,11 +37482,6 @@ ...@@ -37976,11 +37482,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="FSB" override="1"> <Residue name="FSB" override="1">
...@@ -38056,11 +37557,6 @@ ...@@ -38056,11 +37557,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="FgL" override="1"> <Residue name="FgL" override="1">
...@@ -38138,11 +37634,6 @@ ...@@ -38138,11 +37634,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="FsA" override="1"> <Residue name="FsA" override="1">
...@@ -38218,11 +37709,6 @@ ...@@ -38218,11 +37709,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="FsB" override="1"> <Residue name="FsB" override="1">
...@@ -38298,11 +37784,6 @@ ...@@ -38298,11 +37784,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GGL" override="1"> <Residue name="GGL" override="1">
...@@ -38380,11 +37861,6 @@ ...@@ -38380,11 +37861,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GSA" override="1"> <Residue name="GSA" override="1">
...@@ -38460,11 +37936,6 @@ ...@@ -38460,11 +37936,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GSB" override="1"> <Residue name="GSB" override="1">
...@@ -38540,11 +38011,6 @@ ...@@ -38540,11 +38011,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GgL" override="1"> <Residue name="GgL" override="1">
...@@ -38622,11 +38088,6 @@ ...@@ -38622,11 +38088,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GsA" override="1"> <Residue name="GsA" override="1">
...@@ -38702,11 +38163,6 @@ ...@@ -38702,11 +38163,6 @@
<Bond atomName1="C9" atomName2="O9" /> <Bond atomName1="C9" atomName2="O9" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="GsB" override="1"> <Residue name="GsB" override="1">
...@@ -38782,11 +38238,6 @@ ...@@ -38782,11 +38238,6 @@
<Bond atomName1="O8" atomName2="H8O" /> <Bond atomName1="O8" atomName2="H8O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
</Residue> </Residue>
<Residue name="HGL" override="1"> <Residue name="HGL" override="1">
...@@ -38864,11 +38315,6 @@ ...@@ -38864,11 +38315,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="HSA" override="1"> <Residue name="HSA" override="1">
...@@ -38944,11 +38390,6 @@ ...@@ -38944,11 +38390,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="HSB" override="1"> <Residue name="HSB" override="1">
...@@ -39024,11 +38465,6 @@ ...@@ -39024,11 +38465,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="HgL" override="1"> <Residue name="HgL" override="1">
...@@ -39106,11 +38542,6 @@ ...@@ -39106,11 +38542,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="HsA" override="1"> <Residue name="HsA" override="1">
...@@ -39186,11 +38617,6 @@ ...@@ -39186,11 +38617,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="HsB" override="1"> <Residue name="HsB" override="1">
...@@ -39266,11 +38692,6 @@ ...@@ -39266,11 +38692,6 @@
<Bond atomName1="O9" atomName2="H9O" /> <Bond atomName1="O9" atomName2="H9O" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
</Residue> </Residue>
<Residue name="IGL" override="1"> <Residue name="IGL" override="1">
...@@ -39348,12 +38769,7 @@ ...@@ -39348,12 +38769,7 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ISA" override="1"> <Residue name="ISA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -39428,12 +38844,7 @@ ...@@ -39428,12 +38844,7 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="ISB" override="1"> <Residue name="ISB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -39508,12 +38919,7 @@ ...@@ -39508,12 +38919,7 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="IgL" override="1"> <Residue name="IgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -39590,12 +38996,7 @@ ...@@ -39590,12 +38996,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="IsA" override="1"> <Residue name="IsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -39670,12 +39071,7 @@ ...@@ -39670,12 +39071,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="IsB" override="1"> <Residue name="IsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -39750,12 +39146,7 @@ ...@@ -39750,12 +39146,7 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O9" /> <ExternalBond atomName="O9" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JGL" override="1"> <Residue name="JGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -39832,12 +39223,7 @@ ...@@ -39832,12 +39223,7 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JSA" override="1"> <Residue name="JSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -39912,12 +39298,7 @@ ...@@ -39912,12 +39298,7 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JSB" override="1"> <Residue name="JSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -39992,12 +39373,7 @@ ...@@ -39992,12 +39373,7 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JgL" override="1"> <Residue name="JgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -40074,12 +39450,7 @@ ...@@ -40074,12 +39450,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JsA" override="1"> <Residue name="JsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -40154,12 +39525,7 @@ ...@@ -40154,12 +39525,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="JsB" override="1"> <Residue name="JsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -40234,12 +39600,7 @@ ...@@ -40234,12 +39600,7 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O8" /> <ExternalBond atomName="O8" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KGL" override="1"> <Residue name="KGL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -40316,12 +39677,7 @@ ...@@ -40316,12 +39677,7 @@
<Bond atomName1="OHG" atomName2="HOG" /> <Bond atomName1="OHG" atomName2="HOG" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KSA" override="1"> <Residue name="KSA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -40396,12 +39752,7 @@ ...@@ -40396,12 +39752,7 @@
<Bond atomName1="CME" atomName2="H1M" /> <Bond atomName1="CME" atomName2="H1M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KSB" override="1"> <Residue name="KSB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -40476,12 +39827,7 @@ ...@@ -40476,12 +39827,7 @@
<Bond atomName1="C3" atomName2="H3A" /> <Bond atomName1="C3" atomName2="H3A" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KgL" override="1"> <Residue name="KgL" override="1">
<Atom name="C2" type="glycam-Cy" charge="-0.014" /> <Atom name="C2" type="glycam-Cy" charge="-0.014" />
...@@ -40558,12 +39904,7 @@ ...@@ -40558,12 +39904,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KsA" override="1"> <Residue name="KsA" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.237" /> <Atom name="C2" type="glycam-Cy" charge="0.237" />
...@@ -40638,12 +39979,7 @@ ...@@ -40638,12 +39979,7 @@
<Bond atomName1="C3" atomName2="H3E" /> <Bond atomName1="C3" atomName2="H3E" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="KsB" override="1"> <Residue name="KsB" override="1">
<Atom name="C2" type="glycam-Cy" charge="0.09" /> <Atom name="C2" type="glycam-Cy" charge="0.09" />
...@@ -40718,12 +40054,7 @@ ...@@ -40718,12 +40054,7 @@
<Bond atomName1="CME" atomName2="H3M" /> <Bond atomName1="CME" atomName2="H3M" />
<ExternalBond atomName="C2" /> <ExternalBond atomName="C2" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="C1" />
<ExternalBond atomName="O1A" />
<ExternalBond atomName="O1B" />
<ExternalBond atomName="O7" /> <ExternalBond atomName="O7" />
<ExternalBond atomName="C5N" />
<ExternalBond atomName="O5N" />
</Residue> </Residue>
<Residue name="MEX" override="1"> <Residue name="MEX" override="1">
<Atom name="CH3" type="glycam-Cg" charge="0.233" /> <Atom name="CH3" type="glycam-Cg" charge="0.233" />
...@@ -48030,9 +47361,6 @@ ...@@ -48030,9 +47361,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -48073,9 +47401,6 @@ ...@@ -48073,9 +47401,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -48360,9 +47685,6 @@ ...@@ -48360,9 +47685,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -48403,9 +47725,6 @@ ...@@ -48403,9 +47725,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -48518,9 +47837,6 @@ ...@@ -48518,9 +47837,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -48561,9 +47877,6 @@ ...@@ -48561,9 +47877,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49444,9 +48757,6 @@ ...@@ -49444,9 +48757,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49487,9 +48797,6 @@ ...@@ -49487,9 +48797,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49774,9 +49081,6 @@ ...@@ -49774,9 +49081,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49817,9 +49121,6 @@ ...@@ -49817,9 +49121,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49932,9 +49233,6 @@ ...@@ -49932,9 +49233,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -49975,9 +49273,6 @@ ...@@ -49975,9 +49273,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
...@@ -56748,9 +56043,6 @@ ...@@ -56748,9 +56043,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WOB" override="1"> <Residue name="WOB" override="1">
...@@ -56792,9 +56084,6 @@ ...@@ -56792,9 +56084,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WPA" override="1"> <Residue name="WPA" override="1">
...@@ -57266,9 +56555,6 @@ ...@@ -57266,9 +56555,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WUB" override="1"> <Residue name="WUB" override="1">
...@@ -57310,9 +56596,6 @@ ...@@ -57310,9 +56596,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WVA" override="1"> <Residue name="WVA" override="1">
...@@ -57770,9 +57053,6 @@ ...@@ -57770,9 +57053,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WZB" override="1"> <Residue name="WZB" override="1">
...@@ -57814,9 +57094,6 @@ ...@@ -57814,9 +57094,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WaA" override="1"> <Residue name="WaA" override="1">
...@@ -59258,9 +58535,6 @@ ...@@ -59258,9 +58535,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WoB" override="1"> <Residue name="WoB" override="1">
...@@ -59302,9 +58576,6 @@ ...@@ -59302,9 +58576,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WpA" override="1"> <Residue name="WpA" override="1">
...@@ -59776,9 +59047,6 @@ ...@@ -59776,9 +59047,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WuB" override="1"> <Residue name="WuB" override="1">
...@@ -59820,9 +59088,6 @@ ...@@ -59820,9 +59088,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WvA" override="1"> <Residue name="WvA" override="1">
...@@ -60280,9 +59545,6 @@ ...@@ -60280,9 +59545,6 @@
<Bond atomName1="O2" atomName2="H2O" /> <Bond atomName1="O2" atomName2="H2O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="WzB" override="1"> <Residue name="WzB" override="1">
...@@ -60324,9 +59586,6 @@ ...@@ -60324,9 +59586,6 @@
<Bond atomName1="C6" atomName2="O6B" /> <Bond atomName1="C6" atomName2="O6B" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="XEA" override="1"> <Residue name="XEA" override="1">
...@@ -62488,9 +61747,6 @@ ...@@ -62488,9 +61747,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YOB" override="1"> <Residue name="YOB" override="1">
...@@ -62532,9 +61788,6 @@ ...@@ -62532,9 +61788,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YQA" override="1"> <Residue name="YQA" override="1">
...@@ -62908,9 +62161,6 @@ ...@@ -62908,9 +62161,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YUB" override="1"> <Residue name="YUB" override="1">
...@@ -62952,9 +62202,6 @@ ...@@ -62952,9 +62202,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YXA" override="1"> <Residue name="YXA" override="1">
...@@ -63070,9 +62317,6 @@ ...@@ -63070,9 +62317,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YZB" override="1"> <Residue name="YZB" override="1">
...@@ -63114,9 +62358,6 @@ ...@@ -63114,9 +62358,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YaA" override="1"> <Residue name="YaA" override="1">
...@@ -64018,9 +63259,6 @@ ...@@ -64018,9 +63259,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YoB" override="1"> <Residue name="YoB" override="1">
...@@ -64062,9 +63300,6 @@ ...@@ -64062,9 +63300,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YqA" override="1"> <Residue name="YqA" override="1">
...@@ -64438,9 +63673,6 @@ ...@@ -64438,9 +63673,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YuB" override="1"> <Residue name="YuB" override="1">
...@@ -64482,9 +63714,6 @@ ...@@ -64482,9 +63714,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YxA" override="1"> <Residue name="YxA" override="1">
...@@ -64600,9 +63829,6 @@ ...@@ -64600,9 +63829,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="YzB" override="1"> <Residue name="YzB" override="1">
...@@ -64644,9 +63870,6 @@ ...@@ -64644,9 +63870,6 @@
<Bond atomName1="O3" atomName2="H3O" /> <Bond atomName1="O3" atomName2="H3O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O4" /> <ExternalBond atomName="O4" />
</Residue> </Residue>
<Residue name="ZAA" override="1"> <Residue name="ZAA" override="1">
...@@ -65696,9 +64919,6 @@ ...@@ -65696,9 +64919,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
<Residue name="ZOB" override="1"> <Residue name="ZOB" override="1">
...@@ -65740,9 +64960,6 @@ ...@@ -65740,9 +64960,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
<Residue name="ZQA" override="1"> <Residue name="ZQA" override="1">
...@@ -66108,9 +65325,6 @@ ...@@ -66108,9 +65325,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
<Residue name="ZUB" override="1"> <Residue name="ZUB" override="1">
...@@ -66152,9 +65366,6 @@ ...@@ -66152,9 +65366,6 @@
<Bond atomName1="C2" atomName2="O2" /> <Bond atomName1="C2" atomName2="O2" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
<Residue name="ZXA" override="1"> <Residue name="ZXA" override="1">
...@@ -66344,9 +65555,6 @@ ...@@ -66344,9 +65555,6 @@
<Bond atomName1="O4" atomName2="H4O" /> <Bond atomName1="O4" atomName2="H4O" />
<ExternalBond atomName="C1" /> <ExternalBond atomName="C1" />
<ExternalBond atomName="O2" /> <ExternalBond atomName="O2" />
<ExternalBond atomName="C6" />
<ExternalBond atomName="O6A" />
<ExternalBond atomName="O6B" />
<ExternalBond atomName="O3" /> <ExternalBond atomName="O3" />
</Residue> </Residue>
<Residue name="HYP" override="1"> <Residue name="HYP" override="1">
...@@ -66639,8 +65847,8 @@ ...@@ -66639,8 +65847,8 @@
<Bond atomName1="CG" atomName2="ND2" /> <Bond atomName1="CG" atomName2="ND2" />
<Bond atomName1="ND2" atomName2="HD21" /> <Bond atomName1="ND2" atomName2="HD21" />
<Bond atomName1="C" atomName2="O" /> <Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="ND2" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<ExternalBond atomName="ND2" />
</Residue> </Residue>
<Residue name="NOLP" override="1"> <Residue name="NOLP" override="1">
<Atom name="N" type="protein-N3" charge="-0.202" /> <Atom name="N" type="protein-N3" charge="-0.202" />
...@@ -66675,8 +65883,8 @@ ...@@ -66675,8 +65883,8 @@
<Bond atomName1="CA" atomName2="HA" /> <Bond atomName1="CA" atomName2="HA" />
<Bond atomName1="CA" atomName2="C" /> <Bond atomName1="CA" atomName2="C" />
<Bond atomName1="C" atomName2="O" /> <Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OD1" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<ExternalBond atomName="OD1" />
</Residue> </Residue>
<Residue name="NOLS" override="1"> <Residue name="NOLS" override="1">
<Atom name="N" type="protein-N3" charge="0.1849" /> <Atom name="N" type="protein-N3" charge="0.1849" />
...@@ -66702,8 +65910,8 @@ ...@@ -66702,8 +65910,8 @@
<Bond atomName1="CB" atomName2="HB3" /> <Bond atomName1="CB" atomName2="HB3" />
<Bond atomName1="CB" atomName2="OG" /> <Bond atomName1="CB" atomName2="OG" />
<Bond atomName1="C" atomName2="O" /> <Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OG" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<ExternalBond atomName="OG" />
</Residue> </Residue>
<Residue name="NOLT" override="1"> <Residue name="NOLT" override="1">
<Atom name="N" type="protein-N3" charge="0.1812" /> <Atom name="N" type="protein-N3" charge="0.1812" />
...@@ -66735,8 +65943,8 @@ ...@@ -66735,8 +65943,8 @@
<Bond atomName1="CG2" atomName2="HG22" /> <Bond atomName1="CG2" atomName2="HG22" />
<Bond atomName1="CG2" atomName2="HG23" /> <Bond atomName1="CG2" atomName2="HG23" />
<Bond atomName1="C" atomName2="O" /> <Bond atomName1="C" atomName2="O" />
<ExternalBond atomName="OG1" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<ExternalBond atomName="OG1" />
</Residue> </Residue>
</Residues> </Residues>
<HarmonicBondForce> <HarmonicBondForce>
...@@ -67895,31 +67103,29 @@ for force in sys.getForces(): ...@@ -67895,31 +67103,29 @@ for force in sys.getForces():
from openmm.app.internal import compiled from openmm.app.internal import compiled
   
class GlycamTemplateMatcher(object): class GlycamTemplateMatcher(object):
def __init__(self, glycam_residues):
self.glycam_residues = glycam_residues
   
def __init__(self, glycam_residues): def __call__(self, ff, residue, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles):
self.glycam_residues = glycam_residues if residue.name in self.glycam_residues:
template = ff._templates[residue.name]
def __call__(self, ff, residue, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles): if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
if residue.name in self.glycam_residues: return template
template = ff._templates[residue.name]
if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
return template
   
# The residue doesn't actually match the template with the same name. Try the terminal variants. # The residue doesn't actually match the template with the same name. Try the terminal variants.
   
if 'N'+residue.name in self.glycam_residues: if "N" + residue.name in self.glycam_residues:
template = ff._templates['N'+residue.name] template = ff._templates["N" + residue.name]
if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None: if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
return template return template
if 'C'+residue.name in self.glycam_residues: if "C" + residue.name in self.glycam_residues:
template = ff._templates['C'+residue.name] template = ff._templates["C" + residue.name]
if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None: if compiled.matchResidueToTemplate(residue, template, bondedToAtom, ignoreExternalBonds, ignoreExtraParticles) is not None:
return template return template
return None return None
   
glycam_residues = set() glycam_residues = set()
for residue in tree.getroot().find('Residues').findall('Residue'): for residue in tree.getroot().find("Residues").findall("Residue"):
glycam_residues.add(residue.get('name')) glycam_residues.add(residue.get("name"))
self.registerTemplateMatcher(GlycamTemplateMatcher(glycam_residues)) self.registerTemplateMatcher(GlycamTemplateMatcher(glycam_residues))
</InitializationScript> </InitializationScript></ForceField>
</ForceField> \ No newline at end of file
wrappers/python/openmm/app/data/amber19-all.xml 0 → 100644
View file @ 0f78d025
<ForceField>
<Include file="amber19/protein.ff19SB.xml"/>
<Include file="amber19/DNA.OL21.xml"/>
<Include file="amber14/RNA.OL3.xml"/>
</ForceField>
wrappers/python/openmm/app/data/amber19/DNA.OL21.xml 0 → 100644
View file @ 0f78d025
<ForceField>
<Info>
<DateGenerated>2025-04-30</DateGenerated>
<Source Source="./files/DNA.OL21/leaprc.DNA.OL21" md5hash="0d0c0ad847034aa80e4dacd33830b168" sourcePackage="AmberTools" sourcePackageVersion="24.8">./files/DNA.OL21/leaprc.DNA.OL21</Source>
<Reference>Zgarbova, M.; Sponer, J.; Jurecka, P. Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER. J. Chem. Theory Comput., 2021, 17, 6292-6301.</Reference>
</Info>
<AtomTypes>
<Type element="C" name="DNA-C" class="DNA-C" mass="12.01"/>
<Type element="C" name="DNA-CA" class="DNA-CA" mass="12.01"/>
<Type element="C" name="DNA-CB" class="DNA-CB" mass="12.01"/>
<Type element="C" name="DNA-CK" class="DNA-CK" mass="12.01"/>
<Type element="C" name="DNA-CM" class="DNA-CM" mass="12.01"/>
<Type element="C" name="DNA-CQ" class="DNA-CQ" mass="12.01"/>
<Type element="C" name="DNA-CT" class="DNA-CT" mass="12.01"/>
<Type element="H" name="DNA-H" class="DNA-H" mass="1.008"/>
<Type element="H" name="DNA-HC" class="DNA-HC" mass="1.008"/>
<Type element="H" name="DNA-H1" class="DNA-H1" mass="1.008"/>
<Type element="H" name="DNA-H2" class="DNA-H2" mass="1.008"/>
<Type element="H" name="DNA-HA" class="DNA-HA" mass="1.008"/>
<Type element="H" name="DNA-H4" class="DNA-H4" mass="1.008"/>
<Type element="H" name="DNA-H5" class="DNA-H5" mass="1.008"/>
<Type element="H" name="DNA-HO" class="DNA-HO" mass="1.008"/>
<Type element="N" name="DNA-NA" class="DNA-NA" mass="14.01"/>
<Type element="N" name="DNA-NB" class="DNA-NB" mass="14.01"/>
<Type element="N" name="DNA-NC" class="DNA-NC" mass="14.01"/>
<Type element="N" name="DNA-N2" class="DNA-N2" mass="14.01"/>
<Type element="N" name="DNA-N*" class="DNA-N*" mass="14.01"/>
<Type element="O" name="DNA-O" class="DNA-O" mass="16.0"/>
<Type element="O" name="DNA-O2" class="DNA-O2" mass="16.0"/>
<Type element="O" name="DNA-OH" class="DNA-OH" mass="16.0"/>
<Type element="O" name="DNA-OS" class="DNA-OS" mass="16.0"/>
<Type element="P" name="DNA-P" class="DNA-P" mass="30.97"/>
<Type element="C" name="DNA-C7" class="DNA-C7" mass="12.01"/>
<Type element="C" name="DNA-C2" class="DNA-C2" mass="12.01"/>
<Type element="C" name="DNA-C1" class="DNA-C1" mass="12.01"/>
<Type element="C" name="DNA-CJ" class="DNA-CJ" mass="12.01"/>
</AtomTypes>
<Residues>
<Residue name="DA">
<Atom name="P" type="DNA-P" charge="1.1659"/>
<Atom name="OP1" type="DNA-O2" charge="-0.7761"/>
<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
<Atom name="O5'" type="DNA-OS" charge="-0.4954"/>
<Atom name="C5'" type="DNA-CJ" charge="-0.0069"/>
<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
<Atom name="H1'" type="DNA-H2" charge="0.1838"/>
<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
<Atom name="C8" type="DNA-C2" charge="0.1607"/>
<Atom name="H8" type="DNA-H5" charge="0.1877"/>
<Atom name="N7" type="DNA-NB" charge="-0.6175"/>
<Atom name="C5" type="DNA-CB" charge="0.0725"/>
<Atom name="C6" type="DNA-CA" charge="0.6897"/>
<Atom name="N6" type="DNA-N2" charge="-0.9123"/>
<Atom name="H61" type="DNA-H" charge="0.4167"/>
<Atom name="H62" type="DNA-H" charge="0.4167"/>
<Atom name="N1" type="DNA-NC" charge="-0.7624"/>
<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
<Atom name="H2" type="DNA-H5" charge="0.0598"/>
<Atom name="N3" type="DNA-NC" charge="-0.7417"/>
<Atom name="C4" type="DNA-CB" charge="0.38"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
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<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
<Bond atomName1="N7" atomName2="C5"/>
<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N6" atomName2="H61"/>
<Bond atomName1="N6" atomName2="H62"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
<Bond atomName1="N3" atomName2="C4"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DA3">
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<Atom name="OP1" type="DNA-O2" charge="-0.7761"/>
<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
<Atom name="O5'" type="DNA-OS" charge="-0.4954"/>
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<Atom name="H5'" type="DNA-H1" charge="0.0754"/>
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<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
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<Atom name="N9" type="DNA-N*" charge="-0.0268"/>
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<Atom name="C2" type="DNA-CQ" charge="0.5716"/>
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<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
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<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
<Bond atomName1="N9" atomName2="C4"/>
<Bond atomName1="C8" atomName2="H8"/>
<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="N6"/>
<Bond atomName1="C6" atomName2="N1"/>
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<Bond atomName1="C2" atomName2="H2"/>
<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DA5">
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<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
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<Atom name="C1'" type="DNA-CT" charge="0.0431"/>
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</Residue>
<Residue name="DAN">
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</Residue>
<Residue name="DC">
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<ExternalBond atomName="P"/>
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</Residue>
<Residue name="DC3">
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<Bond atomName1="P" atomName2="OP1"/>
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<Bond atomName1="N1" atomName2="C6"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="O3'" atomName2="HO3'"/>
<ExternalBond atomName="P"/>
</Residue>
<Residue name="DC5">
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<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
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<Atom name="C4" type="DNA-CA" charge="0.8439"/>
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<Atom name="H41" type="DNA-H" charge="0.4314"/>
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<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OS" charge="-0.5232"/>
<Bond atomName1="HO5'" atomName2="O5'"/>
<Bond atomName1="O5'" atomName2="C5'"/>
<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N1"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C6" atomName2="H6"/>
<Bond atomName1="C6" atomName2="C5"/>
<Bond atomName1="C5" atomName2="H5"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C4" atomName2="N4"/>
<Bond atomName1="C4" atomName2="N3"/>
<Bond atomName1="N4" atomName2="H41"/>
<Bond atomName1="N4" atomName2="H42"/>
<Bond atomName1="N3" atomName2="C2"/>
<Bond atomName1="C2" atomName2="O2"/>
<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DCN">
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<Atom name="O5'" type="DNA-OH" charge="-0.6318"/>
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<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
<Atom name="C4'" type="DNA-CT" charge="0.1629"/>
<Atom name="H4'" type="DNA-H1" charge="0.1176"/>
<Atom name="O4'" type="DNA-OS" charge="-0.3691"/>
<Atom name="C1'" type="DNA-CT" charge="-0.0116"/>
<Atom name="H1'" type="DNA-H2" charge="0.1963"/>
<Atom name="N1" type="DNA-N*" charge="-0.0339"/>
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<Atom name="H5" type="DNA-HA" charge="0.1863"/>
<Atom name="C4" type="DNA-CA" charge="0.8439"/>
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<Atom name="H42" type="DNA-H" charge="0.4314"/>
<Atom name="N3" type="DNA-NC" charge="-0.7748"/>
<Atom name="C2" type="DNA-C" charge="0.7959"/>
<Atom name="O2" type="DNA-O" charge="-0.6548"/>
<Atom name="C3'" type="DNA-C7" charge="0.0713"/>
<Atom name="H3'" type="DNA-H1" charge="0.0985"/>
<Atom name="C2'" type="DNA-CT" charge="-0.0854"/>
<Atom name="H2'" type="DNA-HC" charge="0.0718"/>
<Atom name="H2''" type="DNA-HC" charge="0.0718"/>
<Atom name="O3'" type="DNA-OH" charge="-0.6549"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N1"/>
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<Bond atomName1="N1" atomName2="C6"/>
<Bond atomName1="N1" atomName2="C2"/>
<Bond atomName1="C6" atomName2="H6"/>
<Bond atomName1="C6" atomName2="C5"/>
<Bond atomName1="C5" atomName2="H5"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C4" atomName2="N4"/>
<Bond atomName1="C4" atomName2="N3"/>
<Bond atomName1="N4" atomName2="H41"/>
<Bond atomName1="N4" atomName2="H42"/>
<Bond atomName1="N3" atomName2="C2"/>
<Bond atomName1="C2" atomName2="O2"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
</Residue>
<Residue name="DG">
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<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
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<Atom name="H8" type="DNA-H5" charge="0.1997"/>
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<Atom name="O6" type="DNA-O" charge="-0.5699"/>
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<Bond atomName1="P" atomName2="OP1"/>
<Bond atomName1="P" atomName2="OP2"/>
<Bond atomName1="P" atomName2="O5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
<Bond atomName1="O4'" atomName2="C1'"/>
<Bond atomName1="C1'" atomName2="H1'"/>
<Bond atomName1="C1'" atomName2="N9"/>
<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="C5" atomName2="C6"/>
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<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="N2" atomName2="H22"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="C2'" atomName2="H2''"/>
<ExternalBond atomName="P"/>
<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DG3">
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<ExternalBond atomName="P"/>
</Residue>
<Residue name="DG5">
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<Bond atomName1="C8" atomName2="H8"/>
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<Bond atomName1="C6" atomName2="N1"/>
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<ExternalBond atomName="O3'"/>
</Residue>
<Residue name="DGN">
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<Bond atomName1="C4'" atomName2="O4'"/>
<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="C5" atomName2="C6"/>
<Bond atomName1="C5" atomName2="C4"/>
<Bond atomName1="C6" atomName2="O6"/>
<Bond atomName1="C6" atomName2="N1"/>
<Bond atomName1="N1" atomName2="H1"/>
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<Bond atomName1="C2" atomName2="N2"/>
<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="N2" atomName2="H22"/>
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<Bond atomName1="C3'" atomName2="H3'"/>
<Bond atomName1="C3'" atomName2="C2'"/>
<Bond atomName1="C3'" atomName2="O3'"/>
<Bond atomName1="C2'" atomName2="H2'"/>
<Bond atomName1="C2'" atomName2="H2''"/>
<Bond atomName1="O3'" atomName2="HO3'"/>
</Residue>
<Residue name="DT">
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<Atom name="OP1" type="DNA-O2" charge="-0.7761"/>
<Atom name="OP2" type="DNA-O2" charge="-0.7761"/>
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<Atom name="H5''" type="DNA-H1" charge="0.0754"/>
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<Proper class1="DNA-C7" class2="DNA-CT" class3="DNA-CJ" class4="DNA-OS" periodicity1="1" phase1="2.90541469920992" k1="1.86911832" periodicity2="2" phase2="4.290316007374901" k2="1.6072836" periodicity3="3" phase3="6.0031297754045765" k3="3.14394128" periodicity4="4" phase4="4.817632334279947" k4="0.58337512" periodicity5="5" phase5="5.32784443451545" k5="0.18250608000000001" periodicity6="6" phase6="2.464195464305754" k6="0.16058192"/>
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<Proper class1="DNA-CT" class2="DNA-CJ" class3="DNA-OS" class4="DNA-P" periodicity1="1" phase1="0.4115165235620262" k1="2.2089428000000004" periodicity2="2" phase2="3.9033934419015024" k2="0.381890416" periodicity3="3" phase3="3.1696404437351924" k3="2.24067844" periodicity4="4" phase4="3.755617461332694" k4="0.33371584"/>
<Improper class1="DNA-C" class2="" class3="" class4="DNA-O" periodicity1="2" phase1="3.141592653589793" k1="43.932"/>
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<Improper class1="DNA-N2" class2="" class3="" class4="DNA-H" periodicity1="2" phase1="3.141592653589793" k1="4.184"/>
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</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom class="DNA-C" sigma="0.3399669508423535" epsilon="0.359824"/>
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<Atom class="DNA-N2" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-N*" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
<Atom class="DNA-O" sigma="0.2959921901149463" epsilon="0.87864"/>
<Atom class="DNA-O2" sigma="0.2959921901149463" epsilon="0.87864"/>
<Atom class="DNA-OH" sigma="0.3066473387839048" epsilon="0.8803136"/>
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<Atom class="DNA-C2" sigma="0.3399669508423535" epsilon="0.359824"/>
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</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/amber19/opc.xml 0 → 100644
View file @ 0f78d025
<ForceField>
<Info>
<Reference>Izadi S, Anandakrishnan R, Onufriev AV. Building Water Models: A Different Approach. The Journal of Physical Chemistry Letters. 2014 Nov 6;5(21):3863-71. DOI:10.1021/jz501780a</Reference>
<!-- Li/Merz ion parameters of atomic ions for the OPC water model (12-6 set) -->
<DateGenerated>2022-09-28T04:59:42.378081</DateGenerated>
<Source Source="parm/frcmod.ionslm_126_opc" md5hash="61ee47ec99a7ebf66cf09e899a8f0581" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">parm/frcmod.ionslm_126_opc</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">lib/atomic_ions.lib</Source>
</Info>
<AtomTypes>
<Type name="opc-O" class="OW" element="O" mass="16.00000"/>
<Type name="opc-H" class="HW" element="H" mass="1.00800"/>
<Type name="opc-M" class="MW" mass="0"/>
<Type class="ionslm_126_opc-Li+" element="Li" mass="6.94" name="ionslm_126_opc-Li+"/>
<Type class="ionslm_126_opc-Na+" element="Na" mass="22.99" name="ionslm_126_opc-Na+"/>
<Type class="ionslm_126_opc-K+" element="K" mass="39.10" name="ionslm_126_opc-K+"/>
<Type class="ionslm_126_opc-Rb+" element="Rb" mass="85.47" name="ionslm_126_opc-Rb+"/>
<Type class="ionslm_126_opc-Cs+" element="Cs" mass="132.91" name="ionslm_126_opc-Cs+"/>
<Type class="ionslm_126_opc-Tl+" element="Tl" mass="204.38" name="ionslm_126_opc-Tl+"/>
<Type class="ionslm_126_opc-Cu+" element="Cu" mass="63.55" name="ionslm_126_opc-Cu+"/>
<Type class="ionslm_126_opc-Ag+" element="Ag" mass="107.87" name="ionslm_126_opc-Ag+"/>
<Type class="ionslm_126_opc-F-" element="F" mass="19.00" name="ionslm_126_opc-F-"/>
<Type class="ionslm_126_opc-Cl-" element="Cl" mass="35.45" name="ionslm_126_opc-Cl-"/>
<Type class="ionslm_126_opc-Br-" element="Br" mass="79.90" name="ionslm_126_opc-Br-"/>
<Type class="ionslm_126_opc-I-" element="I" mass="126.9" name="ionslm_126_opc-I-"/>
<Type class="ionslm_126_opc-Be2+" element="Be" mass="9.01" name="ionslm_126_opc-Be2+"/>
<Type class="ionslm_126_opc-Cu2+" element="Cu" mass="63.55" name="ionslm_126_opc-Cu2+"/>
<Type class="ionslm_126_opc-Ni2+" element="Ni" mass="58.69" name="ionslm_126_opc-Ni2+"/>
<Type class="ionslm_126_opc-Pt2+" element="Pt" mass="195.08" name="ionslm_126_opc-Pt2+"/>
<Type class="ionslm_126_opc-Zn2+" element="Zn" mass="65.4" name="ionslm_126_opc-Zn2+"/>
<Type class="ionslm_126_opc-Co2+" element="Co" mass="58.93" name="ionslm_126_opc-Co2+"/>
<Type class="ionslm_126_opc-Pd2+" element="Pd" mass="106.42" name="ionslm_126_opc-Pd2+"/>
<Type class="ionslm_126_opc-Ag2+" element="Ag" mass="107.87" name="ionslm_126_opc-Ag2+"/>
<Type class="ionslm_126_opc-Cr2+" element="Cr" mass="52.00" name="ionslm_126_opc-Cr2+"/>
<Type class="ionslm_126_opc-Fe2+" element="Fe" mass="55.85" name="ionslm_126_opc-Fe2+"/>
<Type class="ionslm_126_opc-Mg2+" element="Mg" mass="24.305" name="ionslm_126_opc-Mg2+"/>
<Type class="ionslm_126_opc-V2+" element="V" mass="50.94" name="ionslm_126_opc-V2+"/>
<Type class="ionslm_126_opc-Mn2+" element="Mn" mass="54.94" name="ionslm_126_opc-Mn2+"/>
<Type class="ionslm_126_opc-Hg2+" element="Hg" mass="200.59" name="ionslm_126_opc-Hg2+"/>
<Type class="ionslm_126_opc-Cd2+" element="Cd" mass="112.41" name="ionslm_126_opc-Cd2+"/>
<Type class="ionslm_126_opc-Yb2+" element="Yb" mass="173.05" name="ionslm_126_opc-Yb2+"/>
<Type class="ionslm_126_opc-Ca2+" element="Ca" mass="40.08" name="ionslm_126_opc-Ca2+"/>
<Type class="ionslm_126_opc-Sn2+" element="Sn" mass="118.71" name="ionslm_126_opc-Sn2+"/>
<Type class="ionslm_126_opc-Pb2+" element="Pb" mass="207.2" name="ionslm_126_opc-Pb2+"/>
<Type class="ionslm_126_opc-Eu2+" element="Eu" mass="151.96" name="ionslm_126_opc-Eu2+"/>
<Type class="ionslm_126_opc-Sr2+" element="Sr" mass="87.62" name="ionslm_126_opc-Sr2+"/>
<Type class="ionslm_126_opc-Sm2+" element="Sm" mass="150.36" name="ionslm_126_opc-Sm2+"/>
<Type class="ionslm_126_opc-Ba2+" element="Ba" mass="137.33" name="ionslm_126_opc-Ba2+"/>
<Type class="ionslm_126_opc-Ra2+" element="Ra" mass="226.03" name="ionslm_126_opc-Ra2+"/>
<Type class="ionslm_126_opc-Al3+" element="Al" mass="26.98" name="ionslm_126_opc-Al3+"/>
<Type class="ionslm_126_opc-Fe3+" element="Fe" mass="55.85" name="ionslm_126_opc-Fe3+"/>
<Type class="ionslm_126_opc-Cr3+" element="Cr" mass="52.00" name="ionslm_126_opc-Cr3+"/>
<Type class="ionslm_126_opc-In3+" element="In" mass="114.82" name="ionslm_126_opc-In3+"/>
<Type class="ionslm_126_opc-Tl3+" element="Tl" mass="204.38" name="ionslm_126_opc-Tl3+"/>
<Type class="ionslm_126_opc-Y3+" element="Y" mass="88.91" name="ionslm_126_opc-Y3+"/>
<Type class="ionslm_126_opc-La3+" element="La" mass="138.91" name="ionslm_126_opc-La3+"/>
<Type class="ionslm_126_opc-Ce3+" element="Ce" mass="140.12" name="ionslm_126_opc-Ce3+"/>
<Type class="ionslm_126_opc-Pr3+" element="Pr" mass="140.91" name="ionslm_126_opc-Pr3+"/>
<Type class="ionslm_126_opc-Nd3+" element="Nd" mass="144.24" name="ionslm_126_opc-Nd3+"/>
<Type class="ionslm_126_opc-Sm3+" element="Sm" mass="150.36" name="ionslm_126_opc-Sm3+"/>
<Type class="ionslm_126_opc-Eu3+" element="Eu" mass="151.96" name="ionslm_126_opc-Eu3+"/>
<Type class="ionslm_126_opc-Gd3+" element="Gd" mass="157.25" name="ionslm_126_opc-Gd3+"/>
<Type class="ionslm_126_opc-Tb3+" element="Tb" mass="158.93" name="ionslm_126_opc-Tb3+"/>
<Type class="ionslm_126_opc-Dy3+" element="Dy" mass="162.5" name="ionslm_126_opc-Dy3+"/>
<Type class="ionslm_126_opc-Er3+" element="Er" mass="167.26" name="ionslm_126_opc-Er3+"/>
<Type class="ionslm_126_opc-Tm3+" element="Tm" mass="168.93" name="ionslm_126_opc-Tm3+"/>
<Type class="ionslm_126_opc-Lu3+" element="Lu" mass="174.97" name="ionslm_126_opc-Lu3+"/>
<Type class="ionslm_126_opc-Hf4+" element="Hf" mass="178.49" name="ionslm_126_opc-Hf4+"/>
<Type class="ionslm_126_opc-Zr4+" element="Zr" mass="91.22" name="ionslm_126_opc-Zr4+"/>
<Type class="ionslm_126_opc-Ce4+" element="Ce" mass="140.12" name="ionslm_126_opc-Ce4+"/>
<Type class="ionslm_126_opc-U4+" element="U" mass="238.03" name="ionslm_126_opc-U4+"/>
<Type class="ionslm_126_opc-Pu4+" element="Pu" mass="244.06" name="ionslm_126_opc-Pu4+"/>
<Type class="ionslm_126_opc-Th4+" element="Th" mass="232.04" name="ionslm_126_opc-Th4+"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="O" type="opc-O" charge="0"/>
<Atom name="H1" type="opc-H" charge="0.679142"/>
<Atom name="H2" type="opc-H" charge="0.679142"/>
<Atom name="M" type="opc-M" charge="-1.358284"/>
<!-- weight2 = 0.15939833/(2*(cos(angle/2) * 0.87243313)) -->
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.7045587810585758" weight2="0.1477206094707121" weight3="0.1477206094707121"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
</Residue>
<Residue name="AG1">
<Atom charge="1.0" name="AG1" type="ionslm_126_opc-Ag+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="ionslm_126_opc-Ag2+"/>
</Residue>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="ionslm_126_opc-Al3+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="ionslm_126_opc-Ba2+"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="ionslm_126_opc-Be2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="ionslm_126_opc-Br-"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="ionslm_126_opc-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="ionslm_126_opc-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="ionslm_126_opc-Ce3+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="ionslm_126_opc-Ce4+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="ionslm_126_opc-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="ionslm_126_opc-Co2+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="ionslm_126_opc-Cr2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="ionslm_126_opc-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="ionslm_126_opc-Cs+"/>
</Residue>
<Residue name="CU1">
<Atom charge="1.0" name="CU1" type="ionslm_126_opc-Cu+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="ionslm_126_opc-Cu2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="ionslm_126_opc-Dy3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="ionslm_126_opc-Er3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="ionslm_126_opc-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="ionslm_126_opc-Eu3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="ionslm_126_opc-F-"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="ionslm_126_opc-Fe2+"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="ionslm_126_opc-Fe3+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="ionslm_126_opc-Gd3+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="ionslm_126_opc-Hf4+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="ionslm_126_opc-Hg2+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="ionslm_126_opc-I-"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="ionslm_126_opc-In3+"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="ionslm_126_opc-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="ionslm_126_opc-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="ionslm_126_opc-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="ionslm_126_opc-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="ionslm_126_opc-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="ionslm_126_opc-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="ionslm_126_opc-Na+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="ionslm_126_opc-Nd3+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="ionslm_126_opc-Ni2+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="ionslm_126_opc-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="ionslm_126_opc-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="ionslm_126_opc-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="ionslm_126_opc-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="ionslm_126_opc-Pu4+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="ionslm_126_opc-Ra2+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="ionslm_126_opc-Rb+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="ionslm_126_opc-Sm2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="ionslm_126_opc-Sm3+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="ionslm_126_opc-Sn2+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="ionslm_126_opc-Sr2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="ionslm_126_opc-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="ionslm_126_opc-Th4+"/>
</Residue>
<Residue name="TL1">
<Atom charge="1.0" name="TL1" type="ionslm_126_opc-Tl+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="ionslm_126_opc-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="ionslm_126_opc-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="ionslm_126_opc-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="ionslm_126_opc-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="ionslm_126_opc-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="ionslm_126_opc-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="ionslm_126_opc-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="ionslm_126_opc-Zr4+"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.087243313" k="502416.0"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- angle = arccos(1 - (1.37120510**2 / (2*0.87243313**2))) -->
<Angle class1="HW" class2="OW" class3="HW" angle="1.8081424254418306" k="628.02"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<!-- sigma = (1.777167268 * 2 / (2**(1/6)))*unit.angstrom/unit.nanometer -->
<!-- epsilon = (0.2128008130*unit.kilocalorie)/(unit.kilojoule) -->
<Atom type="opc-O" sigma="0.3166552081964338" epsilon="0.8903586015920001"/>
<Atom type="opc-H" sigma="0.08908987181403394" epsilon="0"/>
<Atom type="opc-M" sigma="0.08908987181403394" epsilon="0"/>
<Atom epsilon="0.009039866720000001" sigma="0.2212992415860603" type="ionslm_126_opc-Li+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.12386075112" sigma="0.2613896839023756" type="ionslm_126_opc-Na+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.58382766144" sigma="0.3032619236549715" type="ionslm_126_opc-K+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.9537620464000001" sigma="0.3239307739158274" type="ionslm_126_opc-Rb+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Cs+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.47070573208000005" sigma="0.29577837442259264" type="ionslm_126_opc-Tl+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.0032724319200000004" sigma="0.21025209748112006" type="ionslm_126_opc-Cu+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.025210566480000002" sigma="0.23448454261453733" type="ionslm_126_opc-Ag+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.0313754556" sigma="0.3278507282756449" type="ionslm_126_opc-F-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.8400519208" sigma="0.4205041949622401" type="ionslm_126_opc-Cl-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.17863094952" sigma="0.4452711793265416" type="ionslm_126_opc-Br-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.77817463544" sigma="0.5167212565213968" type="ionslm_126_opc-I-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="5.35552e-06" sigma="0.16410354388145051" type="ionslm_126_opc-Be2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0031585016" sigma="0.20989573799386393" type="ionslm_126_opc-Cu2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00439211216" sigma="0.21328115312279727" type="ionslm_126_opc-Ni2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00631378152" sigma="0.21720110748261476" type="ionslm_126_opc-Pt2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00631378152" sigma="0.21720110748261476" type="ionslm_126_opc-Zn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.012329536720000001" sigma="0.2250410162022497" type="ionslm_126_opc-Co2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.013433485120000001" sigma="0.2261100946640181" type="ionslm_126_opc-Pd2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="ionslm_126_opc-Ag2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.025210566480000002" sigma="0.23448454261453733" type="ionslm_126_opc-Cr2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="ionslm_126_opc-Fe2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0299963512" sigma="0.23697905902533029" type="ionslm_126_opc-Mg2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.03148911872" sigma="0.23769177799984254" type="ionslm_126_opc-V2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.053825486400000004" sigma="0.2460662259503617" type="ionslm_126_opc-Mn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.053825486400000004" sigma="0.2460662259503617" type="ionslm_126_opc-Hg2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.05861307024" sigma="0.24749166389938626" type="ionslm_126_opc-Cd2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="ionslm_126_opc-Yb2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc-Ca2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="ionslm_126_opc-Sn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="ionslm_126_opc-Pb2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.73715046696" sigma="0.312349090580003" type="ionslm_126_opc-Eu2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="ionslm_126_opc-Sr2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="ionslm_126_opc-Sm2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Ba2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Ra2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.010193772080000002" sigma="0.22272467953508485" type="ionslm_126_opc-Al3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.06572013816000001" sigma="0.249451641079295" type="ionslm_126_opc-Fe3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="ionslm_126_opc-Cr3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.09715545064" sigma="0.2565788308244177" type="ionslm_126_opc-In3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="ionslm_126_opc-Tl3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Y3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5781589690400001" sigma="0.30290556416771536" type="ionslm_126_opc-La3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.65093680392" sigma="0.30736005775841707" type="ionslm_126_opc-Ce3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.62720034432" sigma="0.30593461980939257" type="ionslm_126_opc-Pr3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.47580293192" sigma="0.29613473390984874" type="ionslm_126_opc-Nd3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.41662062848000003" sigma="0.2918584200627751" type="ionslm_126_opc-Sm3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.43586389048" sigma="0.2932838580117997" type="ionslm_126_opc-Eu3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc-Gd3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc-Tb3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.29778189072" sigma="0.2820585341632314" type="ionslm_126_opc-Dy3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Er3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Tm3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.25163082264000003" sigma="0.27760404057252974" type="ionslm_126_opc-Lu3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.11751709584" sigma="0.26032060544060714" type="ionslm_126_opc-Hf4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14799067408" sigma="0.265131458518565" type="ionslm_126_opc-Zr4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5310938643199999" sigma="0.2998765085260382" type="ionslm_126_opc-Ce4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5310938643199999" sigma="0.2998765085260382" type="ionslm_126_opc-U4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="ionslm_126_opc-Pu4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.58952354984" sigma="0.3036182831422276" type="ionslm_126_opc-Th4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/amber19/opc3.xml 0 → 100644
View file @ 0f78d025
<ForceField>
<Info>
<DateGenerated>2022-06-21</DateGenerated>
<Reference>Izadi S, Onufriev AV. Accuracy limit of rigid 3-point water models. The Journal of Chemical Physics 145, 074501 (2016); DOI:10.1063/1.4960175</Reference>
<!-- Li/Merz ion parameters of atomic ions for the OPC3 water model (12-6 set) -->
<DateGenerated>2022-09-28T04:59:42.433215</DateGenerated>
<Source Source="parm/frcmod.ionslm_126_opc3" md5hash="5764d233aceb45e3c28df84ac16d1085" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">parm/frcmod.ionslm_126_opc3</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">lib/atomic_ions.lib</Source>
</Info>
<AtomTypes>
<Type name="opc3-O" class="OW" element="O" mass="16.00000"/>
<Type name="opc3-H" class="HW" element="H" mass="1.00800"/>
<Type class="ionslm_126_opc3-Li+" element="Li" mass="6.94" name="ionslm_126_opc3-Li+"/>
<Type class="ionslm_126_opc3-Na+" element="Na" mass="22.99" name="ionslm_126_opc3-Na+"/>
<Type class="ionslm_126_opc3-K+" element="K" mass="39.10" name="ionslm_126_opc3-K+"/>
<Type class="ionslm_126_opc3-Rb+" element="Rb" mass="85.47" name="ionslm_126_opc3-Rb+"/>
<Type class="ionslm_126_opc3-Cs+" element="Cs" mass="132.91" name="ionslm_126_opc3-Cs+"/>
<Type class="ionslm_126_opc3-Tl+" element="Tl" mass="204.38" name="ionslm_126_opc3-Tl+"/>
<Type class="ionslm_126_opc3-Cu+" element="Cu" mass="63.55" name="ionslm_126_opc3-Cu+"/>
<Type class="ionslm_126_opc3-Ag+" element="Ag" mass="107.87" name="ionslm_126_opc3-Ag+"/>
<Type class="ionslm_126_opc3-F-" element="F" mass="19.00" name="ionslm_126_opc3-F-"/>
<Type class="ionslm_126_opc3-Cl-" element="Cl" mass="35.45" name="ionslm_126_opc3-Cl-"/>
<Type class="ionslm_126_opc3-Br-" element="Br" mass="79.90" name="ionslm_126_opc3-Br-"/>
<Type class="ionslm_126_opc3-I-" element="I" mass="126.9" name="ionslm_126_opc3-I-"/>
<Type class="ionslm_126_opc3-Be2+" element="Be" mass="9.01" name="ionslm_126_opc3-Be2+"/>
<Type class="ionslm_126_opc3-Cu2+" element="Cu" mass="63.55" name="ionslm_126_opc3-Cu2+"/>
<Type class="ionslm_126_opc3-Ni2+" element="Ni" mass="58.69" name="ionslm_126_opc3-Ni2+"/>
<Type class="ionslm_126_opc3-Pt2+" element="Pt" mass="195.08" name="ionslm_126_opc3-Pt2+"/>
<Type class="ionslm_126_opc3-Zn2+" element="Zn" mass="65.4" name="ionslm_126_opc3-Zn2+"/>
<Type class="ionslm_126_opc3-Co2+" element="Co" mass="58.93" name="ionslm_126_opc3-Co2+"/>
<Type class="ionslm_126_opc3-Pd2+" element="Pd" mass="106.42" name="ionslm_126_opc3-Pd2+"/>
<Type class="ionslm_126_opc3-Ag2+" element="Ag" mass="107.87" name="ionslm_126_opc3-Ag2+"/>
<Type class="ionslm_126_opc3-Cr2+" element="Cr" mass="52.00" name="ionslm_126_opc3-Cr2+"/>
<Type class="ionslm_126_opc3-Fe2+" element="Fe" mass="55.85" name="ionslm_126_opc3-Fe2+"/>
<Type class="ionslm_126_opc3-Mg2+" element="Mg" mass="24.305" name="ionslm_126_opc3-Mg2+"/>
<Type class="ionslm_126_opc3-V2+" element="V" mass="50.94" name="ionslm_126_opc3-V2+"/>
<Type class="ionslm_126_opc3-Mn2+" element="Mn" mass="54.94" name="ionslm_126_opc3-Mn2+"/>
<Type class="ionslm_126_opc3-Hg2+" element="Hg" mass="200.59" name="ionslm_126_opc3-Hg2+"/>
<Type class="ionslm_126_opc3-Cd2+" element="Cd" mass="112.41" name="ionslm_126_opc3-Cd2+"/>
<Type class="ionslm_126_opc3-Yb2+" element="Yb" mass="173.05" name="ionslm_126_opc3-Yb2+"/>
<Type class="ionslm_126_opc3-Ca2+" element="Ca" mass="40.08" name="ionslm_126_opc3-Ca2+"/>
<Type class="ionslm_126_opc3-Sn2+" element="Sn" mass="118.71" name="ionslm_126_opc3-Sn2+"/>
<Type class="ionslm_126_opc3-Pb2+" element="Pb" mass="207.2" name="ionslm_126_opc3-Pb2+"/>
<Type class="ionslm_126_opc3-Eu2+" element="Eu" mass="151.96" name="ionslm_126_opc3-Eu2+"/>
<Type class="ionslm_126_opc3-Sr2+" element="Sr" mass="87.62" name="ionslm_126_opc3-Sr2+"/>
<Type class="ionslm_126_opc3-Sm2+" element="Sm" mass="150.36" name="ionslm_126_opc3-Sm2+"/>
<Type class="ionslm_126_opc3-Ba2+" element="Ba" mass="137.33" name="ionslm_126_opc3-Ba2+"/>
<Type class="ionslm_126_opc3-Ra2+" element="Ra" mass="226.03" name="ionslm_126_opc3-Ra2+"/>
<Type class="ionslm_126_opc3-Al3+" element="Al" mass="26.98" name="ionslm_126_opc3-Al3+"/>
<Type class="ionslm_126_opc3-Fe3+" element="Fe" mass="55.85" name="ionslm_126_opc3-Fe3+"/>
<Type class="ionslm_126_opc3-Cr3+" element="Cr" mass="52.00" name="ionslm_126_opc3-Cr3+"/>
<Type class="ionslm_126_opc3-In3+" element="In" mass="114.82" name="ionslm_126_opc3-In3+"/>
<Type class="ionslm_126_opc3-Tl3+" element="Tl" mass="204.38" name="ionslm_126_opc3-Tl3+"/>
<Type class="ionslm_126_opc3-Y3+" element="Y" mass="88.91" name="ionslm_126_opc3-Y3+"/>
<Type class="ionslm_126_opc3-La3+" element="La" mass="138.91" name="ionslm_126_opc3-La3+"/>
<Type class="ionslm_126_opc3-Ce3+" element="Ce" mass="140.12" name="ionslm_126_opc3-Ce3+"/>
<Type class="ionslm_126_opc3-Pr3+" element="Pr" mass="140.91" name="ionslm_126_opc3-Pr3+"/>
<Type class="ionslm_126_opc3-Nd3+" element="Nd" mass="144.24" name="ionslm_126_opc3-Nd3+"/>
<Type class="ionslm_126_opc3-Sm3+" element="Sm" mass="150.36" name="ionslm_126_opc3-Sm3+"/>
<Type class="ionslm_126_opc3-Eu3+" element="Eu" mass="151.96" name="ionslm_126_opc3-Eu3+"/>
<Type class="ionslm_126_opc3-Gd3+" element="Gd" mass="157.25" name="ionslm_126_opc3-Gd3+"/>
<Type class="ionslm_126_opc3-Tb3+" element="Tb" mass="158.93" name="ionslm_126_opc3-Tb3+"/>
<Type class="ionslm_126_opc3-Dy3+" element="Dy" mass="162.5" name="ionslm_126_opc3-Dy3+"/>
<Type class="ionslm_126_opc3-Er3+" element="Er" mass="167.26" name="ionslm_126_opc3-Er3+"/>
<Type class="ionslm_126_opc3-Tm3+" element="Tm" mass="168.93" name="ionslm_126_opc3-Tm3+"/>
<Type class="ionslm_126_opc3-Lu3+" element="Lu" mass="174.97" name="ionslm_126_opc3-Lu3+"/>
<Type class="ionslm_126_opc3-Hf4+" element="Hf" mass="178.49" name="ionslm_126_opc3-Hf4+"/>
<Type class="ionslm_126_opc3-Zr4+" element="Zr" mass="91.22" name="ionslm_126_opc3-Zr4+"/>
<Type class="ionslm_126_opc3-Ce4+" element="Ce" mass="140.12" name="ionslm_126_opc3-Ce4+"/>
<Type class="ionslm_126_opc3-U4+" element="U" mass="238.03" name="ionslm_126_opc3-U4+"/>
<Type class="ionslm_126_opc3-Pu4+" element="Pu" mass="244.06" name="ionslm_126_opc3-Pu4+"/>
<Type class="ionslm_126_opc3-Th4+" element="Th" mass="232.04" name="ionslm_126_opc3-Th4+"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="O" type="opc3-O" charge="-0.895170"/>
<Atom name="H1" type="opc3-H" charge="0.447585"/>
<Atom name="H2" type="opc3-H" charge="0.447585"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
<Residue name="AG1">
<Atom charge="1.0" name="AG1" type="ionslm_126_opc3-Ag+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="ionslm_126_opc3-Ag2+"/>
</Residue>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="ionslm_126_opc3-Al3+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="ionslm_126_opc3-Ba2+"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="ionslm_126_opc3-Be2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="ionslm_126_opc3-Br-"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="ionslm_126_opc3-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="ionslm_126_opc3-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="ionslm_126_opc3-Ce3+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="ionslm_126_opc3-Ce4+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="ionslm_126_opc3-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="ionslm_126_opc3-Co2+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="ionslm_126_opc3-Cr2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="ionslm_126_opc3-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="ionslm_126_opc3-Cs+"/>
</Residue>
<Residue name="CU1">
<Atom charge="1.0" name="CU1" type="ionslm_126_opc3-Cu+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="ionslm_126_opc3-Cu2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="ionslm_126_opc3-Dy3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="ionslm_126_opc3-Er3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="ionslm_126_opc3-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="ionslm_126_opc3-Eu3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="ionslm_126_opc3-F-"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="ionslm_126_opc3-Fe2+"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="ionslm_126_opc3-Fe3+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="ionslm_126_opc3-Gd3+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="ionslm_126_opc3-Hf4+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="ionslm_126_opc3-Hg2+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="ionslm_126_opc3-I-"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="ionslm_126_opc3-In3+"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="ionslm_126_opc3-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="ionslm_126_opc3-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="ionslm_126_opc3-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="ionslm_126_opc3-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="ionslm_126_opc3-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="ionslm_126_opc3-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="ionslm_126_opc3-Na+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="ionslm_126_opc3-Nd3+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="ionslm_126_opc3-Ni2+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="ionslm_126_opc3-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="ionslm_126_opc3-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="ionslm_126_opc3-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="ionslm_126_opc3-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="ionslm_126_opc3-Pu4+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="ionslm_126_opc3-Ra2+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="ionslm_126_opc3-Rb+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="ionslm_126_opc3-Sm2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="ionslm_126_opc3-Sm3+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="ionslm_126_opc3-Sn2+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="ionslm_126_opc3-Sr2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="ionslm_126_opc3-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="ionslm_126_opc3-Th4+"/>
</Residue>
<Residue name="TL1">
<Atom charge="1.0" name="TL1" type="ionslm_126_opc3-Tl+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="ionslm_126_opc3-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="ionslm_126_opc3-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="ionslm_126_opc3-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="ionslm_126_opc3-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="ionslm_126_opc3-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="ionslm_126_opc3-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="ionslm_126_opc3-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="ionslm_126_opc3-Zr4+"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.0978882" k="502416.0"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) -->
<Angle class1="HW" class2="OW" class3="HW" angle="1.9106321528999624" k="628.02"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<!-- sigma = (1.7814990 * 2 / (2**(1/6)))*unit.angstrom/unit.nanometer -->
<!-- epsilon = (0.163406*unit.kilocalorie)/(unit.kilojoule) -->
<Atom type="opc3-O" sigma="0.31742703509365927" epsilon="0.683690704"/>
<Atom type="opc3-H" sigma="1" epsilon="0"/>
<Atom epsilon="0.013625196" sigma="0.22628827440764618" type="ionslm_126_opc3-Li+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.1260287744" sigma="0.2617460433896317" type="ionslm_126_opc3-Na+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.58667223752" sigma="0.3034401033985996" type="ionslm_126_opc3-K+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.89173069" sigma="0.32072353853052216" type="ionslm_126_opc3-Rb+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.4963237108" sigma="0.35012319622915333" type="ionslm_126_opc3-Cs+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.52838869912" sigma="0.29969832878241015" type="ionslm_126_opc3-Tl+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.004698632" sigma="0.2139938720973095" type="ionslm_126_opc3-Cu+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.0318714108" sigma="0.2378699577434706" type="ionslm_126_opc3-Ag+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.9537620464000001" sigma="0.3239307739158274" type="ionslm_126_opc3-F-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.68724395648" sigma="0.4108824888063245" type="ionslm_126_opc3-Cl-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.18294026032" sigma="0.4456275388137977" type="ionslm_126_opc3-Br-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.64743605776" sigma="0.4953396872860286" type="ionslm_126_opc3-I-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.598264e-05" sigma="0.17301253106285389" type="ionslm_126_opc3-Be2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.007283507200000001" sigma="0.2188047251752673" type="ionslm_126_opc3-Cu2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="ionslm_126_opc3-Ni2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.014015354" sigma="0.22664463389490233" type="ionslm_126_opc3-Pt2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.015669289200000002" sigma="0.22807007184392686" type="ionslm_126_opc3-Zn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.022184153760000002" sigma="0.23270274517825662" type="ionslm_126_opc3-Co2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0230594884" sigma="0.23323728440914082" type="ionslm_126_opc3-Pd2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.033437523840000004" sigma="0.23858267671798283" type="ionslm_126_opc3-Ag2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.03762051968" sigma="0.24036447415426354" type="ionslm_126_opc3-Cr2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.04078617592000001" sigma="0.24161173235966005" type="ionslm_126_opc3-Fe2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.04415701552" sigma="0.2428589905650565" type="ionslm_126_opc3-Mg2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.045666519040000006" sigma="0.2433935297959407" type="ionslm_126_opc3-V2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0727321456" sigma="0.25123343851557567" type="ionslm_126_opc3-Mn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0727321456" sigma="0.25123343851557567" type="ionslm_126_opc3-Hg2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.07494179968" sigma="0.25176797774645987" type="ionslm_126_opc3-Cd2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.37961047072000004" sigma="0.2890075441647261" type="ionslm_126_opc3-Yb2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.39325717248000003" sigma="0.2900766226264945" type="ionslm_126_opc3-Ca2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.423779578" sigma="0.2923929592936593" type="ionslm_126_opc3-Sn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.64496410208" sigma="0.307003698271161" type="ionslm_126_opc3-Pb2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.7982505068" sigma="0.31573450570893624" type="ionslm_126_opc3-Eu2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.8179506616000001" sigma="0.31680358417070464" type="ionslm_126_opc3-Sr2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.8378363768" sigma="0.31787266263247305" type="ionslm_126_opc3-Sm2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.5001257116000002" sigma="0.35030137597278144" type="ionslm_126_opc3-Ba2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.5001257116000002" sigma="0.35030137597278144" type="ionslm_126_opc3-Ra2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.01724489992" sigma="0.22931733004932334" type="ionslm_126_opc3-Al3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.07951189920000001" sigma="0.2528370562082283" type="ionslm_126_opc3-Fe3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="ionslm_126_opc3-Cr3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.10942737368000001" sigma="0.25889516749158265" type="ionslm_126_opc3-In3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.15799491096" sigma="0.2665568964675895" type="ionslm_126_opc3-Tl3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Y3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.67508049224" sigma="0.3087854957074416" type="ionslm_126_opc3-La3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="ionslm_126_opc3-Ce3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.7276888530400001" sigma="0.3118145513491188" type="ionslm_126_opc3-Pr3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.55575929744" sigma="0.3014801262186908" type="ionslm_126_opc3-Nd3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="ionslm_126_opc3-Sm3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.50965295632" sigma="0.2984510705770137" type="ionslm_126_opc3-Eu3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="ionslm_126_opc3-Gd3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.40484250112000003" sigma="0.2909675213446348" type="ionslm_126_opc3-Tb3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc3-Dy3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Er3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Tm3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.29778189072" sigma="0.2820585341632314" type="ionslm_126_opc3-Lu3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14921629320000002" sigma="0.26530963826219306" type="ionslm_126_opc3-Hf4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.17386691496" sigma="0.2686950533911263" type="ionslm_126_opc3-Zr4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.6009964544" sigma="0.3043310021167399" type="ionslm_126_opc3-Ce4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.6009964544" sigma="0.3043310021167399" type="ionslm_126_opc3-U4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.52838869912" sigma="0.29969832878241015" type="ionslm_126_opc3-Pu4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.63901700632" sigma="0.3066473387839048" type="ionslm_126_opc3-Th4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/amber19/protein.ff19SB.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/protein.ff19ipq.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/spce.xml 0 → 100644
View file @ 0f78d025
<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 @ 0f78d025
<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 @ 0f78d025
<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 @ 0f78d025
<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 @ 0f78d025
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip4pew" md5hash="7aa9de49a8df5ebc45f74e1f47d13c2a" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip4pew</Source>
<Source Source="parm/frcmod.ions234lm_126_tip4pew" md5hash="3902b775a0fe5d42cab716a82c183747" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip4pew</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip4pfb.xml" md5hash="5da20fd20f6aefc31c499fc7c635bf69" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip4pfb.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279q13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. (2014). Building force fields - an automatic, systematic and reproducible approach. Journal of Physical Chemistry Letters, 5, 1885-1891.</Reference>
</Info>
<AtomTypes>
<Type class="tip4pfb_standard-Li+" element="Li" mass="6.94" name="tip4pfb_standard-Li+"/>
<Type class="tip4pfb_standard-Na+" element="Na" mass="22.99" name="tip4pfb_standard-Na+"/>
<Type class="tip4pfb_standard-K+" element="K" mass="39.1" name="tip4pfb_standard-K+"/>
<Type class="tip4pfb_standard-Rb+" element="Rb" mass="85.47" name="tip4pfb_standard-Rb+"/>
<Type class="tip4pfb_standard-Cs+" element="Cs" mass="132.91" name="tip4pfb_standard-Cs+"/>
<Type class="tip4pfb_standard-F-" element="F" mass="19.0" name="tip4pfb_standard-F-"/>
<Type class="tip4pfb_standard-Cl-" element="Cl" mass="35.45" name="tip4pfb_standard-Cl-"/>
<Type class="tip4pfb_standard-Br-" element="Br" mass="79.9" name="tip4pfb_standard-Br-"/>
<Type class="tip4pfb_standard-I-" element="I" mass="126.9" name="tip4pfb_standard-I-"/>
<Type class="tip4pfb_standard-Be2+" element="Be" mass="9.01" name="tip4pfb_standard-Be2+"/>
<Type class="tip4pfb_standard-Cu2+" element="Cu" mass="63.55" name="tip4pfb_standard-Cu2+"/>
<Type class="tip4pfb_standard-Ni2+" element="Ni" mass="58.69" name="tip4pfb_standard-Ni2+"/>
<Type class="tip4pfb_standard-Pt2+" element="Pt" mass="195.08" name="tip4pfb_standard-Pt2+"/>
<Type class="tip4pfb_standard-Zn2+" element="Zn" mass="65.4" name="tip4pfb_standard-Zn2+"/>
<Type class="tip4pfb_standard-Co2+" element="Co" mass="58.93" name="tip4pfb_standard-Co2+"/>
<Type class="tip4pfb_standard-Pd2+" element="Pd" mass="106.42" name="tip4pfb_standard-Pd2+"/>
<Type class="tip4pfb_standard-Ag2+" element="Ag" mass="107.87" name="tip4pfb_standard-Ag2+"/>
<Type class="tip4pfb_standard-Cr2+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr2+"/>
<Type class="tip4pfb_standard-Fe2+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe2+"/>
<Type class="tip4pfb_standard-Mg2+" element="Mg" mass="24.305" name="tip4pfb_standard-Mg2+"/>
<Type class="tip4pfb_standard-V2+" element="V" mass="50.94" name="tip4pfb_standard-V2+"/>
<Type class="tip4pfb_standard-Mn2+" element="Mn" mass="54.94" name="tip4pfb_standard-Mn2+"/>
<Type class="tip4pfb_standard-Hg2+" element="Hg" mass="200.59" name="tip4pfb_standard-Hg2+"/>
<Type class="tip4pfb_standard-Cd2+" element="Cd" mass="112.41" name="tip4pfb_standard-Cd2+"/>
<Type class="tip4pfb_standard-Yb2+" element="Yb" mass="173.05" name="tip4pfb_standard-Yb2+"/>
<Type class="tip4pfb_standard-Ca2+" element="Ca" mass="40.08" name="tip4pfb_standard-Ca2+"/>
<Type class="tip4pfb_standard-Sn2+" element="Sn" mass="118.71" name="tip4pfb_standard-Sn2+"/>
<Type class="tip4pfb_standard-Pb2+" element="Pb" mass="207.2" name="tip4pfb_standard-Pb2+"/>
<Type class="tip4pfb_standard-Eu2+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu2+"/>
<Type class="tip4pfb_standard-Sr2+" element="Sr" mass="87.62" name="tip4pfb_standard-Sr2+"/>
<Type class="tip4pfb_standard-Sm2+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm2+"/>
<Type class="tip4pfb_standard-Ba2+" element="Ba" mass="137.33" name="tip4pfb_standard-Ba2+"/>
<Type class="tip4pfb_standard-Ra2+" element="Ra" mass="226.03" name="tip4pfb_standard-Ra2+"/>
<Type class="tip4pfb_standard-Al3+" element="Al" mass="26.98" name="tip4pfb_standard-Al3+"/>
<Type class="tip4pfb_standard-Fe3+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe3+"/>
<Type class="tip4pfb_standard-Cr3+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr3+"/>
<Type class="tip4pfb_standard-In3+" element="In" mass="114.82" name="tip4pfb_standard-In3+"/>
<Type class="tip4pfb_standard-Tl3+" element="Tl" mass="204.38" name="tip4pfb_standard-Tl3+"/>
<Type class="tip4pfb_standard-Y3+" element="Y" mass="88.91" name="tip4pfb_standard-Y3+"/>
<Type class="tip4pfb_standard-La3+" element="La" mass="138.91" name="tip4pfb_standard-La3+"/>
<Type class="tip4pfb_standard-Ce3+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce3+"/>
<Type class="tip4pfb_standard-Pr3+" element="Pr" mass="140.91" name="tip4pfb_standard-Pr3+"/>
<Type class="tip4pfb_standard-Nd3+" element="Nd" mass="144.24" name="tip4pfb_standard-Nd3+"/>
<Type class="tip4pfb_standard-Sm3+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm3+"/>
<Type class="tip4pfb_standard-Eu3+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu3+"/>
<Type class="tip4pfb_standard-Gd3+" element="Gd" mass="157.25" name="tip4pfb_standard-Gd3+"/>
<Type class="tip4pfb_standard-Tb3+" element="Tb" mass="158.93" name="tip4pfb_standard-Tb3+"/>
<Type class="tip4pfb_standard-Dy3+" element="Dy" mass="162.5" name="tip4pfb_standard-Dy3+"/>
<Type class="tip4pfb_standard-Er3+" element="Er" mass="167.26" name="tip4pfb_standard-Er3+"/>
<Type class="tip4pfb_standard-Tm3+" element="Tm" mass="168.93" name="tip4pfb_standard-Tm3+"/>
<Type class="tip4pfb_standard-Lu3+" element="Lu" mass="174.97" name="tip4pfb_standard-Lu3+"/>
<Type class="tip4pfb_standard-Hf4+" element="Hf" mass="178.49" name="tip4pfb_standard-Hf4+"/>
<Type class="tip4pfb_standard-Zr4+" element="Zr" mass="91.22" name="tip4pfb_standard-Zr4+"/>
<Type class="tip4pfb_standard-Ce4+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce4+"/>
<Type class="tip4pfb_standard-U4+" element="U" mass="238.03" name="tip4pfb_standard-U4+"/>
<Type class="tip4pfb_standard-Pu4+" element="Pu" mass="244.06" name="tip4pfb_standard-Pu4+"/>
<Type class="tip4pfb_standard-Th4+" element="Th" mass="232.04" name="tip4pfb_standard-Th4+"/>
<Type name="tip4p-fb-O" class="tip4p-fb-O" element="O" mass="15.99943"/>
<Type name="tip4p-fb-H" class="tip4p-fb-H" element="H" mass="1.007947"/>
<Type name="tip4p-fb-M" class="tip4p-fb-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip4pfb_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip4pfb_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip4pfb_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip4pfb_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip4pfb_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip4pfb_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip4pfb_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip4pfb_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip4pfb_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip4pfb_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip4pfb_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip4pfb_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip4pfb_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip4pfb_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip4pfb_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip4pfb_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip4pfb_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip4pfb_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip4pfb_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip4pfb_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip4pfb_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip4pfb_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip4pfb_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip4pfb_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip4pfb_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip4pfb_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip4pfb_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip4pfb_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip4pfb_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip4pfb_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip4pfb_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip4pfb_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip4pfb_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip4pfb_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip4pfb_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip4pfb_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip4pfb_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip4pfb_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip4pfb_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip4pfb_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip4pfb_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip4pfb_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip4pfb_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip4pfb_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip4pfb_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip4pfb_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip4pfb_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip4pfb_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip4pfb_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip4pfb_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip4pfb_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip4pfb_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip4pfb_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip4pfb_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip4pfb_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip4pfb_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip4pfb_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip4p-fb-O" charge="0"/>
<Atom name="H1" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="H2" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="M" type="tip4p-fb-M" charge="-1.0517362213526e+00"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="8.203146574531e-01" weight2="8.984267127345e-02" weight3="8.984267127345e-02"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip4p-fb-O" type2="tip4p-fb-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip4p-fb-H" type2="tip4p-fb-O" type3="tip4p-fb-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.4350874656" sigma="0.14396923285147886" type="tip4pfb_standard-Li+"/>
<Atom epsilon="0.7047424999999999" sigma="0.21844836568801118" type="tip4pfb_standard-Na+"/>
<Atom epsilon="1.1692819784000001" sigma="0.2833057923686279" type="tip4pfb_standard-K+"/>
<Atom epsilon="1.8122970896000001" sigma="0.304509181860368" type="tip4pfb_standard-Rb+"/>
<Atom epsilon="1.6503026512" sigma="0.3364033559697921" type="tip4pfb_standard-Cs+"/>
<Atom epsilon="0.0065906368" sigma="0.4522201893280362" type="tip4pfb_standard-F-"/>
<Atom epsilon="0.048791716" sigma="0.49177609241346726" type="tip4pfb_standard-Cl-"/>
<Atom epsilon="0.1270986232" sigma="0.4932015303624918" type="tip4pfb_standard-Br-"/>
<Atom epsilon="0.1745071088" sigma="0.5259866031900563" type="tip4pfb_standard-I-"/>
<Atom epsilon="4.853439999999999e-06" sigma="0.1635690046505663" type="tip4pfb_standard-Be2+"/>
<Atom epsilon="0.00424537928" sigma="0.2129247936355411" type="tip4pfb_standard-Cu2+"/>
<Atom epsilon="0.00651925776" sigma="0.21755746696987088" type="tip4pfb_standard-Ni2+"/>
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="tip4pfb_standard-Pt2+"/>
<Atom epsilon="0.01050071032" sigma="0.22308103902234097" type="tip4pfb_standard-Zn2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Co2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Pd2+"/>
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="tip4pfb_standard-Ag2+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr2+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="tip4pfb_standard-Fe2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-Mg2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-V2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Mn2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Hg2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="tip4pfb_standard-Cd2+"/>
<Atom epsilon="0.45559312408" sigma="0.29470929596082424" type="tip4pfb_standard-Yb2+"/>
<Atom epsilon="0.46311578872000003" sigma="0.29524383519170844" type="tip4pfb_standard-Ca2+"/>
<Atom epsilon="0.49648724720000004" sigma="0.29756017185887335" type="tip4pfb_standard-Sn2+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip4pfb_standard-Pb2+"/>
<Atom epsilon="0.9712365224" sigma="0.3248216726339677" type="tip4pfb_standard-Eu2+"/>
<Atom epsilon="0.985288068" sigma="0.32553439160847997" type="tip4pfb_standard-Sr2+"/>
<Atom epsilon="1.02424478992" sigma="0.3274943687883887" type="tip4pfb_standard-Sm2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ba2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ra2+"/>
<Atom epsilon="0.01678206584" sigma="0.22896097056206718" type="tip4pfb_standard-Al3+"/>
<Atom epsilon="0.05043699032" sigma="0.2449971474885933" type="tip4pfb_standard-Fe3+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr3+"/>
<Atom epsilon="0.10650049832000001" sigma="0.2583606282606984" type="tip4pfb_standard-In3+"/>
<Atom epsilon="0.16579982824" sigma="0.2676259749293579" type="tip4pfb_standard-Tl3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Y3+"/>
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="tip4pfb_standard-La3+"/>
<Atom epsilon="0.66295839824" sigma="0.3080727767329294" type="tip4pfb_standard-Ce3+"/>
<Atom epsilon="0.64198735344" sigma="0.30682551852753287" type="tip4pfb_standard-Pr3+"/>
<Atom epsilon="0.49387597096" sigma="0.2973819921152453" type="tip4pfb_standard-Nd3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip4pfb_standard-Sm3+"/>
<Atom epsilon="0.4580931896" sigma="0.29488747570445234" type="tip4pfb_standard-Eu3+"/>
<Atom epsilon="0.35748949536" sigma="0.2872257467284454" type="tip4pfb_standard-Gd3+"/>
<Atom epsilon="0.37289213824" sigma="0.28847300493384187" type="tip4pfb_standard-Tb3+"/>
<Atom epsilon="0.32577870832" sigma="0.28455305057402436" type="tip4pfb_standard-Dy3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Er3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Tm3+"/>
<Atom epsilon="0.28625681168" sigma="0.280989455701463" type="tip4pfb_standard-Lu3+"/>
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="tip4pfb_standard-Hf4+"/>
<Atom epsilon="0.16712607256" sigma="0.26780415467298596" type="tip4pfb_standard-Zr4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-Ce4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-U4+"/>
<Atom epsilon="0.43343181496" sigma="0.29310567826817163" type="tip4pfb_standard-Pu4+"/>
<Atom epsilon="0.5502288444000001" sigma="0.3011237667314347" type="tip4pfb_standard-Th4+"/>
<Atom type="tip4p-fb-O" sigma="3.165552430462e-01" epsilon="7.492790213533e-01"/>
<Atom type="tip4p-fb-H" sigma="1" epsilon="0"/>
<Atom type="tip4p-fb-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024.xml 0 → 100644
View file @ 0f78d025
This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/openmm/app/data/charmm_polar_2023.xml 0 → 100644
View file @ 0f78d025
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wrappers/python/setup.py
View file @ 0f78d025
...@@ -153,7 +153,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM, ...@@ -153,7 +153,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
"openmm.app.internal.pdbx.writer"] "openmm.app.internal.pdbx.writer"]
setupKeywords["data_files"] = [] setupKeywords["data_files"] = []
setupKeywords["package_data"] = {"openmm" : [], setupKeywords["package_data"] = {"openmm" : [],
"openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/charmm36/*.xml', 'data/implicit/*.xml'], "openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/amber19/*.xml', 'data/charmm36/*.xml', 'data/implicit/*.xml'],
"openmm.app.internal" : []} "openmm.app.internal" : []}
setupKeywords["install_requires"] = ["numpy"] setupKeywords["install_requires"] = ["numpy"]
setupKeywords["platforms"] = ["Linux", "Mac OS X", "Windows"] setupKeywords["platforms"] = ["Linux", "Mac OS X", "Windows"]
......
wrappers/python/tests/TestForceField.py
View file @ 0f78d025
...@@ -1336,7 +1336,7 @@ class TestForceField(unittest.TestCase): ...@@ -1336,7 +1336,7 @@ class TestForceField(unittest.TestCase):
def test_Disulfides(self): def test_Disulfides(self):
"""Test that various force fields handle disulfides correctly.""" """Test that various force fields handle disulfides correctly."""
pdb = PDBFile('systems/bpti.pdb') pdb = PDBFile('systems/bpti.pdb')
for ff in ['amber99sb.xml', 'amber14-all.xml', 'charmm36.xml', 'amberfb15.xml', 'amoeba2013.xml']: for ff in ['amber99sb.xml', 'amber14-all.xml', 'amber19-all.xml', 'charmm36.xml', 'charmm36_2024.xml', 'amberfb15.xml', 'amoeba2013.xml']:
forcefield = ForceField(ff) forcefield = ForceField(ff)
system = forcefield.createSystem(pdb.topology) system = forcefield.createSystem(pdb.topology)
......
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