Difference between revisions of "AMBER forcefield"

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This page contains information about the AMBER forcefield. See [[AMBER_--_Assisted_Model_Building_with_Energy_Refinement | the AMBER package]] for
information about the computer code.
==Force field==
==Force field==
<math>E_{\rm total} = \sum_{\rm bonds} K_r (r - r_{eq})^2
<math>E_{\rm total} = \sum_{\rm bonds} K_r (r - r_{eq})^2

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

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 ]






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


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.


External links


  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)