What is AMBER?
AMBER (Assisted Model Building with Energy Refinement) is a package of programs for molecular dynamics simulations of proteins and nucleic acids. AMBER is distributed in two parts: AmberTools and Amber. AmberTools is a collection of freely available programs for biomolecular simulation and analysis. Amber is centered around the pmemd simulations program and is under a restrictive license.
Permission of using AMBER
The AMBER software package is distributed in HKU subjected to a campus licensing agreement. End User must accept the AMBER license agreement terms in order to gain access to the AMBER software. User have to submit ITS form CF-162f (Go to www.its.hku.hk/forms. In “Online Application Forms”, click “Staff” or “Students”) with the signed AMBER EULA. Upon receiving the signed agreement, users will be assigned to the AMBER user group “amber”. Otherwise you will not have permission to run Amber. You may check your group membership with command “groups”:
$ groups
$ student amber
To setup required environment variables for Amber, please use following command or refer to the sample PBS scripts under /share1/amber/sample/:
| System | Amber Version | AmberTools Version | Command |
|---|---|---|---|
| HPC2015 | 16 | 17 | module load amber/impi/16 |
| 18 | 19 | module load amber/impi/19 | |
| 20 | 20 | module load amber/impi/20 | |
| HPC2021 | 20 | 20 | module load amber/20-impi |
Additional Information
Official documentation and tutorials can be obtained from AMBER Website.
Amber Reference Manual: Amber2017, Amber2020
Amber with accelerators: Amber on GPU, Amber on Intel Xeon Phi