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Merge branch 'amoeba' of github.com:peastman/openmm

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docs/usersguide/application.rst
View file @ e9021971
......@@ -660,7 +660,9 @@ amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-
amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
amber03.xml AMBER03\ :cite:`Duan2003`
amber10.xml AMBER10
amoeba2009.xml AMOEBA\ :cite:`Ren2002`
amoeba2009.xml AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead.
amoeba2013.xml AMOEBA 2013\ :cite:`Shi2013`
================= ================================================================================
......@@ -692,15 +694,16 @@ the following files:
.. tabularcolumns:: |l|L|
================= ==============================================================================================
================= =================================================================================================
File Implicit Solvation Model
================= ==============================================================================================
================= =================================================================================================
amber96_obc.xml GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
amber99_obc.xml GBSA-OBC solvation model for use with AMBER99 force fields
amber03_obc.xml GBSA-OBC solvation model for use with AMBER03 force field
amber10_obc.xml GBSA-OBC solvation model for use with AMBER10 force field
amoeba2009_gk.xml Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA force field
================= ==============================================================================================
amoeba2009_gk.xml Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
amoeba2013_gk.xml Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
================= =================================================================================================
For example, to use the GBSA-OBC solvation model with the Amber99SB force field,
......
docs/usersguide/references.bib
View file @ e9021971
......@@ -336,10 +336,20 @@
type = {Journal Article}
}
@article{Shi2013
author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {9},
pages = {4046-4063},
year = {2013},
type = {Journal Article}
}
@article{Shirts2007
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular
Simulations},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
journal = {Journal of Physical Chemistry B},
volume = {111},
pages = {13052-13063},
......
wrappers/python/simtk/openmm/app/data/amoeba2013.xml 0 → 100644
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wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml 0 → 100644
View file @ e9021971
<ForceField>
<Info>
<Source>amoebapro13.prm</Source>
<DateGenerated>2014-03-11</DateGenerated>
<Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
</Info>
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