Molecular Dynamics Simulation of ARSA

Preparation

To prepare the pdb-structure for the molecular dynamics simulation we did all steps mentioned in the task-description and also did 5 rounds of minimization with minimise. We chose two mutations that seem to be interesting:

• Mutation 7 (T409I) which is disease causing.
• Mutation 8 (N440S) which is neutral.

Both proteins showed the same pattern in the structure based mutation analysis: SCWRL predicted, that the H-bond pattern change. SCWRL and FoldX predict a stabilizing effect, while minimise predicts a destabilizing effect.

local preparation with gromacs

To prepare the structure for the long minimization-runs we wrote two scripts.

Script 1:

#!/bin/bash

if [ -z "$1" ]; then 
	echo usage: $0 [name of pdb file without .pdb]
	exit
fi

echo starting pdb2gmx
pdb2gmx -f $1.pdb -o $1.gro -p $1.top -water tip3p -ff amber03 -vsite hydrogens > pdb2gmx.out
wait
echo finished pdb2gmx

echo "######################################################################"

echo editconf
editconf -f $1.gro -o $1_box.gro -bt dodecahedron -d 1.0 > editconf.out
wait
echo finished editconf

echo "######################################################################"

echo genbox
genbox -cp $1_box.gro -cs spc216.gro -p $1.top -o $1_water.gro > genbox.out
wait
echo finished genbox

echo "######################################################################"

echo grompp
grompp -v -f $1_1.mdp -c $1_water.gro -p $1.top -o $1_water.tpr > grompp1.out
wait
echo finished grompp

echo "######################################################################"

echo genion
genion -s $1_water.tpr -o $1_solv.pdb -conc 0.1 -neutral -pname NA+ -nname CL- > genion.out
wait
echo finished genion

echo "######################################################################"

echo Do now:
echo - copy everything after the 13 into a new file
echo - run get_changes with this new file
echo - copy the old top file and make the changes you get from get_changes in the copy

At this point some manual work needs to be done. Then script 2 could be used:

#!/bin/bash

if [ -z "$1" ]; then 
	echo usage: $0 [name of pdb file without .pdb]
	exit
fi

echo grompp
grompp -v -f $1_2.mdp -c $1_solv2.pdb -p $1.top -o $1_solv_min.tpr
wait
echo finished grompp

echo "######################################################################"

echo mdrun
mdrun -v -deffnm $1_solv_min -c $1_solv_min.pdb
wait
echo finished mdrun

echo "######################################################################"

echo genrestr
genrestr -f $1_solv_min.pdb -o $1.itp
wait
echo finished genrestr

echo "######################################################################"

echo grompp
grompp -v -f $1_2.mdp -c $1_solv_min.pdb -p $1.top -o $1_solv_min2.tpr
wait
echo finished grompp

echo "######################################################################"

echo mdrun
mdrun -v -deffnm $1_solv_min2 -c $1_solv_min2.pdb
wait
echo finished mdrun

echo "######################################################################"

echo grompp
grompp -v -f nvt.mdp -c $1_solv_min2.pdb -p $1.top -o $1_nvt.tpr
wait
echo finished grompp

echo "######################################################################"

echo the first long mdrun
mdrun -v -deffnm $1_nvt
wait
echo finished the first long mdrun

echo "######################################################################"

echo grompp
grompp -v -f npt.mdp -c $1_nvt.gro -p $1.top -o $1_npt.tpr
wait
echo finished grompp

echo "######################################################################"

echo the second long mdrun
mdrun -v -deffnm $1_npt
wait
echo finished the second long mdrun

echo "######################################################################"

echo "grompp to prepare for lrz"
grompp -v -f md.mdp -c $1_npt.gro -p $1.top -o $1_md.tpr
wait
echo "finished grompp to prepare for lrz"

echo "######################################################################"

LRZ-runs with gromacs

To run gromacs on the LRZ-cluster we used the following config-file: (TODO: include working config-file)