Difference between revisions of "CD task10 protocol"
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==Script with all analysis steps== |
==Script with all analysis steps== |
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+ | ##!/bin/bash |
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+ | #wildtype |
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− | ##!/bin/bash |
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+ | path=/opt/SS12-Practical/gromacs/bin/ |
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− | |||
+ | EDR="2O4H_chainA_md" |
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− | #wildtype |
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+ | MUT="wt" |
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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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+ | |||
− | $path gmxcheck -c $EDR.tpr |
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+ | #pymol visualization |
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− | gmxcheck -f $EDR.xtc |
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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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− | |||
+ | |||
− | #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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+ | |||
− | |||
− | + | #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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− | #a305e |
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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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− | EDR="A305E_scwrl_mini_md" |
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+ | |||
− | MUT="A305E_scwrl" |
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+ | #fluctuations |
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− | |||
+ | |||
− | echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg |
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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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+ | |||
− | echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg |
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+ | #rewrite trajectories |
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− | echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.xvg |
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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 |
Revision as of 18:13, 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