Molecular Dynamics Simulations (PKU)

Short task description

This week, we will start the molecular dynamics simulation of our protein with the wildtype and two mutations. The simulation will be analyzed at a later time, see the complete task description for details. A journal will probably not be neccessary...

Selected Models

• Wildtype 1J8U --> jop pending
• Mutation ALA322GLY --> run finished in 04:28:48, simulation probably successfull, further checks pending
• Mutation ARG408TRP --> run finished in 04:34:08, simulation successfull

Job submission

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34faw/logs/1J8U_wildtype_MD.out
#SBATCH -D /home/hpc/pr58ni/di34faw/MD/
#SBATCH -J 1J8U_wildtype
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=boidolj@in.tum.de
#SBATCH --export=NONE
#SBATCH --time=10:00:00
source /etc/profile.d/modules.sh
module load gromacs

cd $HOME/
$HOME/AGroS/AGroS /home/hpc/pr58ni/di34faw/Gromacs/Models/1J8U.pdb -dir $HOME/MD/ -threads 32 --scwrlPATH $HOME/SCWRL

intermediate Structures

e.g. for the ARG408TRP mutant (model file mut408.pdb)

• mut408.pdb: input structure with clashing water removed.
• mut408_br.pdb: just the protein, no DNA, crystal water, etc..
• mut408_br_0.pdb: 1 file for every chain, if several are present
• mut408.pdb2: structure with hydrogens removed
• mut408_repair.pdb: correctly numbered
• mut408_repair_0.pdb
• mut408_dna.pdb: extracted DNA, empty in our case
• mut408_water.pdb: contains structural water <15A from the protein
• mut408_sc.pdb: sidechains completed/adjusted with scwrl
• mut408_nh.pdb: removed hydrogens, added structural water (and DNA)
• mut408_solv_tmp.pdb: added ions
• mut408_solv.pdb: duplicate water removed
• mut408_solv.pdb2: just protein and added DNA, input to create individual files for each chain (see next step)
• mut408_solv_0.pdb: used to create restriction files for every chain (only 1 here)
• mut408_solv_min.pdb: structure with minimized solvent (protein fixed)
• mut408_solv_min.pdb2: just protein of previous structure, input to create individual files for each chain (see next step)
• mut408_solv_min_0.pdb: used to create restriction files for every chain (only 1 here)
• mut408_solv_min2.pdb: minimization with only backbone restrained
• mut408_solv_min3.pdb: final minimization before MD runs