Difference between revisions of "CD task10 protocol"
Line 1: | Line 1: | ||
==Script with all analysis steps== |
==Script with all analysis steps== |
||
− | ##!/bin/bash |
+ | ##!/bin/bash |
#wildtype |
#wildtype |
Revision as of 19:13, 5 July 2012
Script with all analysis steps
##!/bin/bash
- wildtype
path=/opt/SS12-Practical/gromacs/bin/ EDR="2O4H_chainA_md" MUT="wt"
- gmxcheck
$path gmxcheck -c $EDR.tpr gmxcheck -f $EDR.xtc
- pymol visualization
echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10
- 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
- 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
- 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
- rewrite trajectories
trjconv -f $EDR.xtc -o $MUT.traj_nojump.xtc -pbc nojump
- calculate rmsd
g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-all-atom-vs-start.xvg
- rmsd only calpha
echo 4 4 0 | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-backbone-vs-start.xvg
- rmsds vs average structure
g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.protein.xtc
- select1
- select4
- radius of gyration
g_gyrate -f $EDR.xtc -s $EDR.tpr -o $MUT.radius-of-gyration.xvg
- 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