CD task10 protocol

Script with all analysis steps

##!/bin/bash 

1. wildtype

path=/opt/SS12-Practical/gromacs/bin/ EDR="2O4H_chainA_md" MUT="wt"

1. gmxcheck

$path gmxcheck -c $EDR.tpr gmxcheck -f $EDR.xtc

1. pymol visualization

echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10

1. energy

echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy

1. min dist between periodic boundaries

echo 1 0| g_mindist -f $EDR.xtc -s $EDR.tpr -od $MUT.minimal-periodic-distance.xvg -pi echo 3 0| g_mindist -f $EDR.xtc -s $EDR.tpr -od $MUT.minimal-periodic-distance_calpha.xvg -pi

1. fluctuations

echo 1 0| g_rmsf -f $EDR.xtc -s $EDR.tpr -o $MUT.rmsf-per-residue.xvg -ox $MUT.average.pdb -oq $MUT.bfactors.pdb -res

1. rewrite trajectories

trjconv -f $EDR.xtc -o $MUT.traj_nojump.xtc -pbc nojump

1. calculate rmsd

g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-all-atom-vs-start.xvg

1. rmsd only calpha

echo 4 4 0 | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-backbone-vs-start.xvg

1. rmsds vs average structure

g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.protein.xtc

1. 1. select1
   2. select4

1. radius of gyration

g_gyrate -f $EDR.xtc -s $EDR.tpr -o $MUT.radius-of-gyration.xvg

1. a305e

EDR="A305E_scwrl_mini_md" MUT="A305E_scwrl"

echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.xvg