Difference between revisions of "AMBER forcefield"

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                             \left [ {C_{ij} \over R_{ij}^{12}} -  
 
                             \left [ {C_{ij} \over R_{ij}^{12}} -  
 
                                     {D_{ij} \over R_{ij}^{10}} \right ] </math>
 
                                     {D_{ij} \over R_{ij}^{10}} \right ] </math>
 +
==Parameters==
 +
====ff94====
 +
*[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)]
 +
====ff96====
 +
====ff98====
 +
====ff99====
 +
*[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)]
 +
====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.
 +
*[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)]
 +
====ff02EP====
 
==External links==
 
==External links==
 
*[http://amber.scripps.edu/dbase.html AMBER parameters]
 
*[http://amber.scripps.edu/dbase.html AMBER parameters]
 
==References==
 
==References==
#[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)]
 
 
#[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)]
 
#[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)]
 
[[category:Force fields]]
 
[[category:Force fields]]

Revision as of 14:26, 12 November 2007

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Force field

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 ]

Parameters

ff94

ff96

ff98

ff99

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.

ff02EP

External links

References

  1. 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)