Difference between revisions of "CD task10 protocol"
From Bioinformatikpedia
(Created page with " ==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 …") |
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==Script with all analysis steps== |
==Script with all analysis steps== |
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| − | ##!/bin/bash |
+ | ##!/bin/bash |
| + | |||
| − | |||
| − | #wildtype |
+ | #wildtype |
| − | path=/opt/SS12-Practical/gromacs/bin/ |
+ | path=/opt/SS12-Practical/gromacs/bin/ |
| − | EDR="2O4H_chainA_md" |
+ | EDR="2O4H_chainA_md" |
| − | MUT="wt" |
+ | MUT="wt" |
| + | |||
| − | |||
| + | |||
| − | |||
| − | #gmxcheck |
+ | #gmxcheck |
| − | $path gmxcheck -c $EDR.tpr |
+ | $path gmxcheck -c $EDR.tpr |
| − | gmxcheck -f $EDR.xtc |
+ | gmxcheck -f $EDR.xtc |
| + | |||
| − | |||
| − | #pymol visualization |
+ | #pymol visualization |
| − | echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10 |
+ | echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10 |
| + | |||
| − | |||
| + | #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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| − | #energy |
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| − | echo |
+ | echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg |
| − | echo |
+ | echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy |
| + | |||
| − | 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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| + | #a305e |
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| − | |||
| + | |||
| − | |||
| + | EDR="A305E_scwrl_mini_md" |
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| − | #a305e |
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| + | MUT="A305E_scwrl" |
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| − | |||
| + | |||
| − | EDR="A305E_scwrl_mini_md" |
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| + | echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg |
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| − | MUT="A305E_scwrl" |
||
| + | echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg |
||
| − | |||
| − | echo |
+ | echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg |
| − | echo |
+ | echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.xvg |
| − | 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 15:16, 4 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 #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
