* $Id: 00readme 34 2015-08-04 21:09:45Z alex $

Toppar files for polarizable model based on the classical Drude
oscillator.

August 2015 release
adm jr.

Included are the toppar stream files to perform calculations with the
classical Drude oscillator polarizable force field.  Each stream file
includes both the topology and parameters for that class of compounds.
In ALL cases the master file, toppar_drude_master_protein_2013c.str,
must initally be streamed, followed by any additional files that are
required.  The master file contains the water model, all ions and the
proteins.

See the test subdirectory for test cases.

drude_may13b.doc contains the CHARMM Drude documentation

Note: This is a force field in development and the coverage is limited.  For
example, at this time only the lipids DPPC and DMPC are available.

toppar_drude_master_protein_2013c.str: master file with water, ions
and protein.  Must be read first in all cases.

toppar_drude_carbohydrate_2013c.str: carbohydrates including polyols,
hexapyranoses and furanoses.  No glycosidic linkages are currently
available.

toppar_drude_lipid_2013c.str: lipids (DPPC and DMPC only)

toppar_drude_model_2013c.str: model compounds used for development of
the majority of the nonbond parameters.  Note that model compounds
specific for the indvidual classes molecules are included in the
respective toppar stream files.

toppar_drude_nucleic_acid_2013c.str: DNA only

NOTE: These parameters are developmental and may change in future
release of the Drude polarizabile force field.

References

Water

SWM4-NDP, negative Drude (this will be the default model): Lamoureux,
G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D.,
Jr., A polarizable model of water for molecular dynamics simulations
of biomolecules, Chemical Physics Letters, 2006, 418: 245-249.

SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander
D. MacKerell, Jr.  "Six-site Polarizable Model of Water Based on the
Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508,
2013

Proteins 

Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and
MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and
Proteins based on the Classical Drude Oscillator,” Journal of
Chemical Theory and Computation, 9: 5430–5449, 2013 DOI:
10.1021/ct400781b, NIHMS53671

Atomic ions

Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I.,
Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating
Monovalent and Divalent Ions in Aqueous Solution Using a Drude
Polarizable Force Field, “Journal of Chemical Theory and Computation,
6: 774–786, 2010

Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B.,
“Simulation study of ion pairing in concentrated aqueous salt
solutions with a polarizable force field,” Faraday Discussions, 160,
135–149, 2013, PMC3695446

Lipids

Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and
Roux, B., “A Polarizable Model for Phosphatidylcholine-Containing
Biological Membranes,” Journal of Physical Chemistry, B.,117:
9142-9160, 2013.

Nucleic Acids

Savelyev, A. and MacKerell, A.D., Jr., “All-Atom Polarizable Force
Field for DNA Based on the Classical Drude Oscillator Model,” Journal
of Computational Chemistry, 35: 1219-1239, 2014, DOI: 10.1002/jcc.23611

Parameters for Monovaletn Ions-DNA Interactions
Savelyev, A. and MacKerell, A.D., Jr., “Balancing the Interactions of Ions,
Water, and DNA in the Drude Polarizable Force Field,” Journal
of Physical Chemistry B, 118: 6742−6757, 2014, DOI: 10.1021/jp503469s

Savelyev, A. and MacKerell, A.D., Jr., “Competition among Li+, Na+, K+, and Rb+
Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36
and Drude Polarizable Force Fields,” Journal of Physical Chemistry B, 119: 4428−4440, 2015,
DOI: 10.1021/acs.jpcb.5b00683

Carbohydrates

Hexapyranoses: Note that revisions to the hexapyranoses are ongoing

Patel, D.S., He, X., and MacKerell, A.D., Jr.,
“Polarizable Empirical Force Field for Hexopyranose Monosaccharides
based on the Classical Drude Oscillator,” Journal of Physical
Chemistry B., ASAP article, 2014, 10.1021/jp412696m, NIHMSID #566721

polyalcohols

He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical
Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI:
10.1002/bip.22286

furanoses

Jana, M. and MacKerell, A.D., Jr., “CHARMM Drude Polarizable Force
Field for Aldopentofuranoses and Methyl-aldopentofuranosides,” Journal
of Physical Chemistry B, 119: 7846-7859, 2015, doi:
10.1021/acs.jpcb.5b01767, PMC4483154

Review

Lopes, P.E.M., B. Roux, R., MacKerell, A.D., Jr. “Molecular modeling
and dynamics studies with explicit inclusion of electronic
polarizability. Theory and applications.” Theoretical Chemistry
Accounts, 124:11-28, 2009, PMC2888514

General method

Anisimov, V.M., Lamoureux, G., Vorobyov, I.V., Huang, N.,
Roux, B. and MacKerell, A.D., Jr. :Determination of Electrostatic
Parameters for a Polarizable Force Field Based on the Classical Drude
Oscillator," Journal of Chemical Theory and Computing, 1:153-168,
2005.

Water model (see POSTIVE DRUDE REFERENCES below)

SWM4-NDP, negative Drude (this will be the default model): Lamoureux,
G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D.,
Jr., A polarizable model of water for molecular dynamics simulations
of biomolecules, Chemical Physics Letters, 2006, 418: 245-249.

SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander
D. MacKerell, Jr.  "Six-site Polarizable Model of Water Based on the
Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508,
2013

Alkanes: 

Igor V. Vorobyov, Victor M. Anisimov and Alexander D. MacKerell,
Jr. "Polarizable Empirical Force Field for Alkanes Based on the
Classical Drude Oscillator Model," Journal of Physical Chemistry B,
109: 18988-18999, 2005.

Anisotropic polarizability model:

Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E., Noskov, S.,
MacKerell, A.D., Jr.  and Roux, B. Atomic Level Anisotropy in the
Electrostatic Modeling of Lone Pairs for a Polarizable Force Field
based on the Classical Drude Oscillator, Journal of Chemical Theory
and Computation, 2: 1587-1597, 2006

Ethers:

Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude
Polarizable Force Fields for Linear and Cyclic Ethers, Journal of
Chemical Theory and Computation, 3: 1120-1133, 2007.

Baker, C. and MacKerell, Jr. A.D., “Polarizability Rescaling and
atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field
for Ethers” Journal of Molecular Modeling, 16: 567-576, 2010,
PMC2818097

Sulfur containing compounds

Zhu, X. and MacKerell, A.D., Jr. “Polarizable Empirical Force Field
for Sulfur-Containing Compounds Based on the Classical Drude
Oscillator Model,” Journal of Computational Chemistry, 12: 2330-2341,
2010. PMC2923574

Alcohols:

Anisimov, V.M., Vorobyov, I.V., Roux, B., and MacKerell, A.D., Jr.
Polarizable empirical force field for the primary and secondary
alcohol series based on the classical Drude model. Journal of Chemical
Theory and Computation, 3, 1927-1946, 2007.

Amides:

Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, A.D., Jr., Roux,
B. "Understanding the Dielectric Properties of Liquid Amides from a
Polarizable Force Field," Journal of Physical Chemistry,
112:3509-3521. 2008, PMID: 18302362

Amide model used in 2013 protein FF

Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr.,
“Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide
Solutions Modeled by the CHARMM Additive and Drude Polarizable Force
Fields,” Journal of Chemical Physics, 139: 084509, 2013, PMC3772949

Aromatics:

Lopes, P., Lamoureux, G., Roux, B., MacKerell, A.D., Jr., "Polarizable
Empirical Force Field for Aromatic Compounds Based on the Classical
Drude Oscillator," Journal of Physical Chemistry, B. 111:2873-2885,
2007

Heterocycles

Lopes, P.E.M., Lamoureux, G., MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds
Based on the Classical Drude Oscillator” Journal of Computational
Chemistry, 30: 1821-1838, 2009, PMC251901

Nucleic Acid Bases

Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., “Development of
CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the
Classical Drude Oscillator Model,” Journal of Physical Chemistry,
B. 115; 580–596, 2011, PMC3166616

Polyalcohols

He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical
Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI:
10.1002/bip.22286

Atomic Ions

Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I.,
Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating
Monovalent and Divalent Ions in Aqueous Solution Using a Drude
Polarizable Force Field, “Journal of Chemical Theory and Computation,
6: 774–786, 2010

Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B.,
“Simulation study of ion pairing in concentrated aqueous salt
solutions with a polarizable force field,” Faraday Discussions, 160,
135–149, 2013,PMC3695446

POSTIVE DRUDE REFERENCES

SWM4-DP, positive Drude (works with ions of Lamoureux and Roux):
Lamoureux, G., MacKerell, A.D., Jr., Roux, B. "A simple polarizable
model of water based on classical Drude oscillators," Journal of
Chemical Physics, 119: 5185-5197, 2003

Ions

Lamoureux, G.; Roux, B. Absolute Hydration Free Energy Scale for
Alkali and Halide Ions Established from Simulations with a Polarizable
Force Field, J. Phys. Chem. B 2006, 110, 3308

