Difference between revisions of "AMBER forcefield"

From SklogWiki
Jump to: navigation, search
m
m (Slight tidy)
 
(5 intermediate revisions by 3 users not shown)
Line 2: Line 2:
 
{{Stub-general}}
 
{{Stub-general}}
 
{{Numeric}}
 
{{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==
 
==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
Line 17: Line 18:
 
==Parameters==
 
==Parameters==
 
====ff94====
 
====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)]
+
<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====
 
====ff96====
 
====ff98====
 
====ff98====
 
====ff99====
 
====ff99====
 
Param99 was developed for organic and biological molecules using the restrained electrostatic potential  (RESP) approach to derive the partial charges:
 
Param99 was developed for organic and biological molecules using the restrained electrostatic potential  (RESP) approach to derive the partial charges:
*[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>[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====
 
====ff02====
The  ff02 force field is a polarisable variant of ff99.
+
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.
The  charges  were  determined  at  the  B3LYP/cc-
+
<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>
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====
 
====ff02EP====
 +
==References==
 +
<references/>
 
==External links==
 
==External links==
*[http://amber.scripps.edu/dbase.html AMBER parameters]
+
*[http://ambermd.org/#ff AMBER parameters]
==References==
+
 
#[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]]

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.
Simeq0.png This article is a 'stub' page, it has no, or next to no, content. It is here at the moment to help form part of the structure of SklogWiki. If you add sufficient material to this article then please remove the {{Stub-general}} template from this page.
40px-Stop hand nuvola.svg.png This page contains numerical values and/or equations. If you intend to use ANY of the numbers or equations found in SklogWiki in any way, you MUST take them from the original published article or book, and cite the relevant source accordingly.

AMBER forcefield [1].

Force field[edit]

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[edit]

ff94[edit]

[2]

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]

External links[edit]