Task8 Hemochromatosis Protocol

Getting started

Setting up AGroS

Get AGroS:

module load git

git clone git://github.com/offmarc/AGroS.git

Add line to .profile

export PATH=$PATH:$HOME/masterprakt/task8/AGroS/

Setting up SCWRL4

Install SCWRL4 into AGroS directory. Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).

ln -s Scwrl4 scwrl

Sample script

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log
#SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/
#SBATCH -J 1a6zC_MD
#SBATCH --partition=mpp1_inter
#SBATCH --get-user-env
#SBATCH --ntasks=16
#SBATCH --mail-type=end
#SBATCH --mail-user=MichaelBernhofer@gmx.de
#SBATCH --export=NONE
#SBATCH --time=02:00:00
source /etc/profile.d/modules.sh
module load gromacs
export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v

note: --partition=mpp1_inter means this is for the test runs!

Let's get serious

Final script for one of the MDS runs (in this case the native protein):

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log
#SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/
#SBATCH -J 1a6zC_MD
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=16
#SBATCH --mail-type=end
#SBATCH --mail-user=MichaelBernhofer@gmx.de
#SBATCH --export=NONE
#SBATCH --time=32:00:00
source /etc/profile.d/modules.sh
module load gromacs
export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v