AMBER Tips

Standard Submission Scripts:

AMBER on Armada:

#!/bin/bash

#$ -N <jobname>
#$ -cwd
#$ -pe threaded <numcores>
##$ -q unlimited

module load amber14

 mpirun -np <numcores> pmemd.MPI -i protein.in -c protein_in.restrt -p protein.prmtop -r protein_out.restrt -x protein.mdcrd

gzip protein.mdcrd

AMBER on Pitzer:

#$ -S /bin/bash
#$ -V
#$ -N <jobname>
#$ -cwd
#$ -pe threaded <numcores>
#$ -q all*

module load amber14

mpirun -np <numcores> pmemd.MPI -i protein.in -c protein_in.restrt -p protein.prmtop -r protein_out. restrt -x protein.mdcrd

gzip protein.mdcrd

General Tips:

Converting PDBs to AMBER format using tleap:

1. Unless required, strip hydrogens and let amber add them again.
2. If you already have a waterbox which you want to keep, use the setBox command setBox <loadpdb_object_name> vdw {a_axis b_axis c_axis}