AMBER forcefield: Difference between revisions
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:''This page contains information about the AMBER [[Force fields |forcefield]]. See [[AMBER_--_Assisted_Model_Building_with_Energy_Refinement | the AMBER package]] for information about the computer code.'' | |||
{{Stub-general}} | |||
{{Numeric}} | |||
'''AMBER forcefield''' <ref>[http://dx.doi.org/10.1016/0010-4655(95)00041-D David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter Kollman "AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Computer Physics Communications '''91''' pp. 1-41 (1995)]</ref>. | |||
==Force field== | |||
<math>E_{\rm total} = \sum_{\rm bonds} K_r (r - r_{eq})^2 | |||
+ \sum_{\rm angles} K_\theta (\theta - \theta_{eq})^2 | |||
+ \sum_{\rm dihedrals} {V_n \over 2} | |||
[1 + {\rm cos}(n\phi - \gamma)] | |||
+ \sum_{i<j} \left [ {A_{ij} \over R_{ij}^{12}} - | |||
{B_{ij} \over R_{ij}^6} + | |||
{q_iq_j \over \epsilon R_{ij}} | |||
\right ] | |||
+ \sum_{\rm H-bonds} | |||
\left [ {C_{ij} \over R_{ij}^{12}} - | |||
{D_{ij} \over R_{ij}^{10}} \right ] </math> | |||
==Parameters== | |||
====ff94==== | |||
<ref>[http://dx.doi.org/10.1021/ja00124a002 Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society '''117''' pp 5179 - 5197 (1995)]</ref> | |||
====ff96==== | |||
====ff98==== | |||
====ff99==== | |||
Param99 was developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges: | |||
<ref>[http://www3.interscience.wiley.com/cgi-bin/abstract/72511509/ABSTRACT Junmei Wang, Piotr Cieplak, Peter A. Kollman "How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?", Journal of Computational Chemistry '''21''' pp. 1049-1074 (2000)]</ref> | |||
====ff02==== | |||
The ff02 force field is a polarisable variant of ff99. The charges were determined at the B3LYP/cc-pVTZ//HF/6-31g* level, and hence are more like "gas-phase" charges. | |||
<ref>[http://dx.doi.org/10.1002/jcc.1065 Piotr Cieplak, James Caldwell and Peter Kollman "Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases", Journal of Computational Chemistry '''22''' pp. 1048-1057 (2001)]</ref> | |||
====ff02EP==== | |||
==References== | ==References== | ||
<references/> | |||
==External links== | |||
*[http://ambermd.org/#ff AMBER parameters] | |||
[[category:Force fields]] | [[category:Force fields]] | ||
Latest revision as of 12:34, 22 November 2015
- This page contains information about the AMBER forcefield. See the AMBER package for information about the computer code.
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AMBER forcefield [1].
Force field[edit]
![{\displaystyle E_{\rm {total}}=\sum _{\rm {bonds}}K_{r}(r-r_{eq})^{2}+\sum _{\rm {angles}}K_{\theta }(\theta -\theta _{eq})^{2}+\sum _{\rm {dihedrals}}{V_{n} \over 2}[1+{\rm {cos}}(n\phi -\gamma )]+\sum _{i<j}\left[{A_{ij} \over R_{ij}^{12}}-{B_{ij} \over R_{ij}^{6}}+{q_{i}q_{j} \over \epsilon R_{ij}}\right]+\sum _{\rm {H-bonds}}\left[{C_{ij} \over R_{ij}^{12}}-{D_{ij} \over R_{ij}^{10}}\right]}](https://wikimedia.org/api/rest_v1/media/math/render/svg/07abb3f2d6f16ca1e1dede075b6faf02bc42b5df)
Parameters[edit]
ff94[edit]
ff96[edit]
ff98[edit]
ff99[edit]
Param99 was developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges: [3]
ff02[edit]
The ff02 force field is a polarisable variant of ff99. The charges were determined at the B3LYP/cc-pVTZ//HF/6-31g* level, and hence are more like "gas-phase" charges. [4]
ff02EP[edit]
References[edit]
- ↑ David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter Kollman "AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Computer Physics Communications 91 pp. 1-41 (1995)
- ↑ Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society 117 pp 5179 - 5197 (1995)
- ↑ Junmei Wang, Piotr Cieplak, Peter A. Kollman "How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?", Journal of Computational Chemistry 21 pp. 1049-1074 (2000)
- ↑ Piotr Cieplak, James Caldwell and Peter Kollman "Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases", Journal of Computational Chemistry 22 pp. 1048-1057 (2001)