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

David A. Pearlman; David A. Case; James W. Caldwell; Wilson S. Ross; Thomas E. Cheatham; Steve DeBolt; David Ferguson; George Seibel; Peter Kollman

doi:10.1016/0010-4655(95)00041-D

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

David A. Pearlman
, David A. Case
, James W. Caldwell
, Wilson S. Ross
, Thomas E. Cheatham
, Steve DeBolt
, David Ferguson
, George Seibel
, Peter Kollman

Medicinal Chemistry

Research output: Contribution to journal › Article › peer-review

2955 Scopus citations

Abstract

We describe the development, current features, and some directions for future development of the AMBER package of computer programs. This package has evolved from a program that was constructed to do Assisted Model Building and Energy Refinement to a group of programs embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.

Original language	English (US)
Pages (from-to)	1-41
Number of pages	41
Journal	Computer Physics Communications
Volume	91
Issue number	1-3
DOIs	https://doi.org/10.1016/0010-4655(95)00041-D
State	Published - Sep 2 1995

Bibliographical note

Funding Information:
Peter Kollman is pleased to acknowledger esearch support from the the NIH (GM-29072 and CA-25644) and the NSF (CHE94-17458)T om Cheatham is a BiotechnologyT rainee. David Case acknowledgeNs IH support( GM-45811).

Keywords

Computer simulations
Free energies
Molecular dynamics
Molecular mechanics
Normal modes

Publisher link

10.1016/0010-4655(95)00041-D

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Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). 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(1-3), 1-41. https://doi.org/10.1016/0010-4655(95)00041-D

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. / Pearlman, David A.; Case, David A.; Caldwell, James W. et al.
In: Computer Physics Communications, Vol. 91, No. 1-3, 02.09.1995, p. 1-41.

Research output: Contribution to journal › Article › peer-review

Pearlman, DA, Case, DA, Caldwell, JW, Ross, WS, Cheatham, TE, DeBolt, S, Ferguson, D, Seibel, G & Kollman, P 1995, '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, vol. 91, no. 1-3, pp. 1-41. https://doi.org/10.1016/0010-4655(95)00041-D

Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S et al. 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. 1995 Sep 2;91(1-3):1-41. doi: 10.1016/0010-4655(95)00041-D

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AU - Ross, Wilson S.

AU - Cheatham, Thomas E.

AU - DeBolt, Steve

AU - Ferguson, David

AU - Seibel, George

AU - Kollman, Peter

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KW - Molecular dynamics

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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

Abstract

Bibliographical note

Keywords

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