Supported Applications

Description

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

Usage

Usage Notes

If Amber is available at your site, the AmberTools installation bundled with the Amber installation with be configured and used in your shell. If your site does not have an Amber license, the standalone AmberTools installation will be configured in your shell.

If for some reason you want to use the standalone AmberTools instead of the version bundled with Amber, you can set AMBERTOOLS_PREFFERED=true in your ~/.sbgrid.conf to override the default setting.

Installation

Primary Citation*

D. A. Case, K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R. Harris, S. Izadi, S. A. Izmailov, K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. R. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, Y. Xiong, Y. Xue, D. M. York, and P. A. Kollman. 2020. AMBER 2020. University of California, San Francisco.
(Note: Use this citation when citing Amber20 or AmberTools20.)

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  *Full citation information available through

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