Difference between revisions of "AMBER forcefield"

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#[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)]
 
==External links==
 
==External links==
*[http://amber.scripps.edu/dbase.html AMBER parameters]
+
*[http://ambermd.org/#ff AMBER parameters]
 +
 
 
[[category:Force fields]]
 
[[category:Force fields]]

Revision as of 12:09, 7 November 2013

This page contains information about the AMBER forcefield. See the AMBER package for information about the computer code.
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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

Param99 was developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges:

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

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)

External links