Difference between revisions of "CD task10 protocol"

From Bioinformatikpedia
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==Script with all analysis steps==
 
==Script with all analysis steps==
  +
##!/bin/bash
   
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#wildtype
##!/bin/bash
 
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path=/opt/SS12-Practical/gromacs/bin/
 
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EDR="2O4H_chainA_md"
#wildtype
 
  +
MUT="wt"
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
 
#gmxcheck
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gmxcheck -f $EDR.xtc
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$path gmxcheck -c $EDR.tpr
 
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#pymol visualization
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
 
  +
 
#energy
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#energy
echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg
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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 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg
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echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg
echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy
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echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy
  +
 
  +
 
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#min dist between periodic boundaries
#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
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
 
echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
+
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
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
  +
  +
  +
#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"
  +
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 18:13, 5 July 2012

Script with all analysis steps

    1. !/bin/bash
  1. wildtype

path=/opt/SS12-Practical/gromacs/bin/ EDR="2O4H_chainA_md" MUT="wt"


  1. gmxcheck

$path gmxcheck -c $EDR.tpr gmxcheck -f $EDR.xtc

  1. pymol visualization

echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10


  1. 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


  1. 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

  1. 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

  1. rewrite trajectories

trjconv -f $EDR.xtc -o $MUT.traj_nojump.xtc -pbc nojump

  1. calculate rmsd

g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-all-atom-vs-start.xvg

  1. rmsd only calpha

echo 4 4 0 | g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.rmsd-backbone-vs-start.xvg


  1. rmsds vs average structure

g_rms -f $MUT.traj_nojump.xtc -s $EDR.tpr -o $MUT.protein.xtc

    1. select1
    2. select4
  1. radius of gyration

g_gyrate -f $EDR.xtc -s $EDR.tpr -o $MUT.radius-of-gyration.xvg



  1. 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