AmberTools25

AmberTools25 is a suite of molecular dynamics tools.

Availability

Cluster	Module/Version
BOSE	ambertools25/24.8
BGSC	N/A

Note: You can simply use module load ambertools25 to activate the most recently installed version of this software.

Included Tools/Uses

This is a list of arguments for the AmberTools25 suite that we wanted to highlight. Use this page or the Amber 2025 Reference Manual for a full list.

Tool	Description
tleap	Tool for preparing Amber simulations
parmed	Tool for preparing Amber simulations
pbsa	Solves Poisson-Boltzmann models
sander	General mooleculary dynamics simulation program
fe-toolkit	Analyze alchemical free energy simulations

Amber Force Fields

The `$AMBERHOME` variable is defined upon running `module load ambertools25`. All available parameter files can be found in these locations:

leaprc files - $AMBERHOME/dat/leap/cmd
lib/off files - $AMBERHOME/dat/leap/lib
frcmod/dat files - $AMBERHOME/dat/leap/parm

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load ambertools25/24.8    # Load AmberTools25
cd $AMBERHOME
make test.serial                 # Test each tool and output successes/failures

Real Example

Has your research group used AmberTools25 in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of AmberTools25.

D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruz eiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan, and K.M. Merz Jr. AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023).