Amber is a software package for molecular dynamics simulations, particularly for proteins, nucleic acids and carbohydrates. It’s also a family of force field for molecular dynamics of biomolecules. The Amber software package is distributed by UCSF subject to a licensing agreement.
Amber 14 CPU version is installed in /app1/centos6.3/gnu/apps/amber14. The following sample scripts show you how to submit Amber14 cpu and gpu parallel jobs:

To submit cpu parallel jobs:

$ qsub cpu_run.sh

------------cpu_run.sh----
#!/bin/bash
#PBS -P Amber_parallel
#PBS -j oe
#PBS -N amber_job

#PBS -q parallel24
#PBS -l select=1:ncpus=24:mpiprocs=24:mem=20GB
cd $PBS_O_WORKDIR;

source /app1/centos6.3/gnu/apps/amber14/amber.sh
np=$(cat ${PBS_NODEFILE} |wc -l);
mpirun -np $np -f ${PBS_NODEFILE} /app1/centos6.3/gnu/apps/amber14/bin/pmemd.MPI -O \
        -i amber_job_1.in \
        -o amber_job_1.out \
        -p amber_job_1.top \
        -c amber_job.rst \
        -r amber_job_1.rst \
        -x amber_job_1.mdcrd \
        -e amber_job_1.en \
        -inf amber_job_1.info

-----------------------------------------

Amber GPU version (pmemd.cuda.MPI) is also enabled in /app1/centos6.3/GPU/apps/amber14 folder on the Gold GPU cluster. Login to gold-c01 and refer to the following sample scripts to create your own script and submit your jobs.

[gold-c01]$ qsub gpu_run.sh

------------gpu_run.sh-------

#PBS -N amberb14_gpu
#PBS -q gpu
#PBS -l select=2:ncpus=12:mpiprocs=2:mem=10GB

cd $PBS_O_WORKDIR;
cat $PBS_NODEFILE > ./hostfile_PBS

np=$(cat ${PBS_NODEFILE} |wc -l);

source /etc/profile.d/rec_modules.sh
module load amber14

export CUDA_VISIBLE_DEVICES=0,1

mpirun -np $np -hostfile hostfile_PBS pmemd.cuda_SPFP.MPI -O \
        -i amber_job_1.in \
        -o amber_job_1.out \
        -p amber_job_1.top \
        -c amber_job.rst \
        -r amber_job_1.rst \
        -x amber_job_1.mdcrd \
        -e amber_job_1.en \
        -inf amber_job_1.info
----------------------------------------

It is advisable to submit all your jobs from your working directory in the high performance parallel file system: /hpctmp2 and /hpctmp.

Various applications in Ambertools, including antechamber and xLeap, and the analysis programs such as cpptraj are available from the MobileVisLab. Just issue these commands: anterhamber, tleap, xleap or cpptraj at the command prompt to start the applications. If the command is “not found”, try “module load amber14_gmp” first and type the command again.

Please email nusit-hpc@nus.edu.sg for any problems or queries.