Difference between revisions of "Task8 Hemochromatosis Protocol"

From Bioinformatikpedia
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(→‎Let's get serious)
 
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== Getting started ==
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Casting spell: Create Protocol Page
  
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<br style="clear:both;">
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=== Setting up AGroS ===
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Get AGroS:
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module load git
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git clone git://github.com/offmarc/AGroS.git
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Add line to .profile
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export PATH=$PATH:$HOME/masterprakt/task8/AGroS/
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<br style="clear:both;">
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=== Setting up SCWRL4 ===
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Install SCWRL4 into AGroS directory.
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Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).
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ln -s Scwrl4 scwrl
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<br style="clear:both;">
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=== Sample script ===
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#!/bin/bash
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#SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log
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#SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/
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#SBATCH -J 1a6zC_MD
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#SBATCH --partition=mpp1_inter
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#SBATCH --get-user-env
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#SBATCH --ntasks=16
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#SBATCH --mail-type=end
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#SBATCH --mail-user=MichaelBernhofer@gmx.de
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#SBATCH --export=NONE
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#SBATCH --time=02:00:00
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source /etc/profile.d/modules.sh
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module load gromacs
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export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
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AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
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note: --partition=mpp1_inter means this is for the test runs!
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<br style="clear:both;">
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== Let's get serious ==
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Final script for one of the MDS runs (in this case the native protein):
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#!/bin/bash
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#SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log
  +
#SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/
  +
#SBATCH -J 1a6zC_MD
  +
#SBATCH --clusters=mpp1
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#SBATCH --get-user-env
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#SBATCH --ntasks=16
  +
#SBATCH --mail-type=end
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#SBATCH --mail-user=MichaelBernhofer@gmx.de
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#SBATCH --export=NONE
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#SBATCH --time=32:00:00
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source /etc/profile.d/modules.sh
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module load gromacs
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export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
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AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
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<br style="clear:both;">

Latest revision as of 12:57, 2 July 2012

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


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