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==
   
##!/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
 
  +
echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg
 
  +
echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
#energy
 
echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg
+
echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg
echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
+
echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy
  +
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"
#a305e
 
  +
MUT="A305E_scwrl"
 
  +
EDR="A305E_scwrl_mini_md"
 
  +
echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg
MUT="A305E_scwrl"
 
  +
echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
 
echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg
+
echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg
echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg
+
echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.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 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