Difference between revisions of "CD task10 protocol"
From Bioinformatikpedia
(→Script with all analysis steps) |
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| − | ==Script with all analysis steps== |
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| − | ##!/bin/bash |
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| − | #wildtype |
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| − | path=/opt/SS12-Practical/gromacs/bin/ |
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| − | EDR="2O4H_chainA_md" |
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| − | MUT="wt" |
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| − | #gmxcheck |
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| − | $path gmxcheck -c $EDR.tpr |
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| − | gmxcheck -f $EDR.xtc |
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| − | #pymol visualization |
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| − | echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10 |
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| + | ==Script with all analysis steps== |
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| + | In this script, all the required commands for the analysis methods are listed. |
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| − | |||
| − | #energy |
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| − | echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg |
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| − | echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg |
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| − | echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg |
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| − | echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy |
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| − | |||
| − | #min dist between periodic boundaries |
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| − | echo 1 0| g_mindist -f $EDR.xtc -s $EDR.tpr -od $MUT.minimal-periodic-distance.xvg -pi |
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| − | echo 3 0| g_mindist -f $EDR.xtc -s $EDR.tpr -od $MUT.minimal-periodic-distance_calpha.xvg -pi |
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| − | |||
| − | #fluctuations |
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| − | 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 |
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| − | |||
| − | #rewrite trajectories |
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| − | trjconv -f $EDR.xtc -o $MUT.traj_nojump.xtc -pbc nojump |
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| − | |||
| − | #calculate rmsd |
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| − | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-all-atom-vs-start.xvg |
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| − | |||
| − | #rmsd only calpha |
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| − | echo 4 4 0 | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-backbone-vs-start.xvg |
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| − | |||
| − | #rmsds vs average structure |
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| − | ##### |
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| − | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.protein.xtc |
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| − | ##select1 |
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| − | ##select4 |
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| − | |||
| − | #radius of gyration |
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| − | g_gyrate -f $EDR.xtc -s $EDR.tpr -o $MUT.radius-of-gyration.xvg |
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| − | #a305e |
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| − | EDR="A305E_scwrl_mini_md" |
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| − | MUT="A305E_scwrl" |
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| − | |||
| − | echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg |
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| − | echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg |
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| − | echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg |
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| − | echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.xvg |
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Revision as of 16:12, 7 July 2012
Script with all analysis steps
In this script, all the required commands for the analysis methods are listed.
