AMBER forcefield - Revision history

Carl McBride: Slight tidy

2015-11-22T11:34:56Z

Slight tidy

← Older revision		Revision as of 13:34, 22 November 2015
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	{{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
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	==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==
	~~#[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)]		<references/>
	==External links==		==External links==
	*[http://ambermd.org/#ff AMBER parameters]		*[http://ambermd.org/#ff AMBER parameters]

	[[category:Force fields]]		[[category:Force fields]]

Carl McBride: /* External links */ Updated external link

2013-11-07T11:09:48Z

External links: Updated external link

← Older revision		Revision as of 13:09, 7 November 2013
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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]]

Carl McBride: Reverted edits by 70.135.118.126 (talk) to last revision by Nice and Tidy

2012-01-04T14:30:47Z

Reverted edits by 70.135.118.126 (talk) to last revision by Nice and Tidy

← Older revision		Revision as of 16:30, 4 January 2012
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	*[http://amber.scripps.edu/dbase.html AMBER parameters]		*[http://amber.scripps.edu/dbase.html AMBER parameters]
	[[category:Force fields]]		[[category:Force fields]]
	~~[http://www.prlog.org/11289974-phone-number-lookup-verizon-phone-number-reverse-lookup-to-get-information-you-need-quickly.html phone number lookup verizon]~~

	~~[http://thetvtopc.com/Reverse_Cell_Phone_Lookup_Number reverse phone lookup verizon]~~

70.135.118.126 at 05:53, 4 January 2012

2012-01-04T05:53:17Z

← Older revision		Revision as of 07:53, 4 January 2012
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	*[http://amber.scripps.edu/dbase.html AMBER parameters]		*[http://amber.scripps.edu/dbase.html AMBER parameters]
	[[category:Force fields]]		[[category:Force fields]]
			[http://www.prlog.org/11289974-phone-number-lookup-verizon-phone-number-reverse-lookup-to-get-information-you-need-quickly.html phone number lookup verizon]

			[http://thetvtopc.com/Reverse_Cell_Phone_Lookup_Number reverse phone lookup verizon]

Nice and Tidy: Placed external links at foot of page.

2008-12-11T18:02:56Z

Placed external links at foot of page.

← Older revision		Revision as of 20:02, 11 December 2008
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	*[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)]		*[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==
			#[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://amber.scripps.edu/dbase.html 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]]

Carl McBride: AMBER moved to AMBER forcefield

2008-02-06T12:01:40Z

AMBER moved to AMBER forcefield

← Older revision	Revision as of 14:01, 6 February 2008
(No difference)

Nice and Tidy at 10:02, 5 February 2008

2008-02-05T10:02:32Z

← Older revision		Revision as of 12:02, 5 February 2008
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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}}		{{Stub-general}}
	{{Numeric}}		{{Numeric}}
	~~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

Dduque: some disambiguation

2008-02-04T14:39:03Z

some disambiguation

← Older revision		Revision as of 16:39, 4 February 2008
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	{{Stub-general}}		{{Stub-general}}
	{{Numeric}}		{{Numeric}}
			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

Carl McBride: /* ff99 */

2007-11-12T14:31:05Z

ff99

← Older revision		Revision as of 16:31, 12 November 2007
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	====ff98====		====ff98====
	====ff99====		====ff99====
			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)]		*[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====		====ff02====
	The ff02 force field is a polarisable variant of ff99.		The ff02 force field is a polarisable variant of ff99.

Carl McBride at 13:26, 12 November 2007

2007-11-12T13:26:35Z

← Older revision		Revision as of 15:26, 12 November 2007
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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]]