Difference between revisions of "CD task10 protocol"
From Bioinformatikpedia
(→Script with all analysis steps) |
|||
Line 1: | Line 1: | ||
− | ==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 |
||
+ | ==Script with all analysis steps== |
||
+ | In this script, all the required commands for the analysis methods are listed. |
||
− | |||
− | #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 |
Revision as of 17:12, 7 July 2012
Script with all analysis steps
In this script, all the required commands for the analysis methods are listed.