Task10 Hemochromatosis Protocol

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Casting Spell: Create Protocol Page


The perl script used for the calculation of all plots informations:

<source lang="perl">

  1. !/usr/bin/perl

use strict; my $file=shift; my $refFile; my $outName=shift; my $fileName=$file . "_md"; $refFile= $file . "_solv.pdb";

$file= $file . "_md.xtc";

    `trjconv -f $file -s $refFile -pbc nojump -o traj_nojump.xtc <<EOF\n0\nEOF`;
   `trjconv -f traj_nojump.xtc -s $refFile -center -o traj_center.xtc <<EOF\n1\n0\nEOF`;
   `trjconv -f traj_center.xtc -s $refFile -fit rot+trans -o traj_norot.xtc <<EOF\n1\n0\nEOF`; 
  1. `trjconv -f traj_norot.xtc -s $refFile -o $outName.pdb <<EOF\n1\nEOF`;
  2. `g_filter -f traj.pdb -s $refFile -ol filtered.pdb -fit -nf 5 <<EOF\n1\nEOF`;

`echo 1 1| g_rms -f traj_nojump.xtc -s $fileName.tpr -o $outName.rmsd-allProt-atom-vs-start.xvg`; `echo 3 3| g_rms -f traj_nojump.xtc -s $fileName.tpr -o $outName.rmsd-ca-vs-start.xvg`;

`echo 1 0 | g_sas -f traj_nojump.xtc -s $fileName.tpr -o $outName.SAS.xvg -oa $outName.atomSAS.xvg -or $outName.resSAS.xvg`; `echo 1 1 | g_hbond -f traj_nojump.xtc -s $fileName.tpr -num $outName.hBondsP2P.xvg`;

`echo 1 12 | g_hbond -f traj_nojump.xtc -s $fileName.tpr -num $outName.hBondsP2W.xvg`;

`g_rama -f traj_nojump.xtc -s $fileName.tpr -o $outName.ramaPlot.xvg`;


  1. RMSD protein protein

`echo 1 1 | g_rms -s $fileName.tpr -f traj_nojump.xtc -f2 traj_nojump.xtc -m rmsd-matrix.xpm`; `xpm2ps -f rmsd-matrix.xpm -o $outName.PP.rmsd-matrix.eps -rainbow blue`; `echo 1 1 | g_cluster -s $fileName.tpr -f traj_norot.xtc -dm rmsd-matrix.xpm -dist $outName.PP.rmsd-dist.xvg -o $outName.PP.clusters.xpm -sz $outName.PP.cluster-sizes.xvg -tr $outName.PP.cluster-transitions.xpm -ntr $outName.PP.cluster-transitions.xvg -clid $outName.PP.cluster-id-over-time.xvg -cl $outName.PP.clusters.pdb -cutoff 0.1 -method gromos`;



  1. RMSD mainchain+MCB twice

`echo 6 6 | g_rms -s $fileName.tpr -f traj_nojump.xtc -f2 traj_nojump.xtc -m rmsd-matrix.xpm`; `xpm2ps -f rmsd-matrix.xpm -o $outName.MCB.rmsd-matrix.eps -rainbow blue`; `echo 6 6 | g_cluster -s $fileName.tpr -f traj_norot.xtc -dm rmsd-matrix.xpm -dist $outName.MCB.rmsd-dist.xvg -o $outName.MCB.clusters.xpm -sz $outName.MCB.cluster-sizes.xvg -tr $outName.MCB.cluster-transitions.xpm -ntr $outName.MCB.cluster-transitions.xvg -clid $outName.MCB.cluster-id-over-time.xvg -cl $outName.MCB.clusters.pdb -cutoff 0.1 -method gromos`;




`echo 13 0 | g_energy -f $fileName.edr -o $outName.pressure.xvg`; system("echo -e '9 0' | g_energy -f $fileName.edr -o $outName.potential.xvg"); `echo 12 0 | g_energy -f $fileName.edr -o $outName.temperature.xvg`; `echo 11 0 | g_energy -f $fileName.edr -o $outName.totalEnergy.xvg`;

`echo 1 0 | g_mindist -f $fileName.xtc -s $fileName.tpr -od $outName.minPeriodicDist.xvg -pi`;

`echo 3 0 | g_mindist -f $fileName.xtc -s $fileName.tpr -od $outName.minPeriodicDistOnlyCA.xvg`;

`echo 1 0 | g_rmsf -f $fileName.xtc -s $fileName.tpr -ox $outName.prot.avg.pdb -oq $outName.prot.bFactor.pdb -o $outName.prot.rmsf.xvg -res`; `echo 3 0 | g_rmsf -f $fileName.xtc -s $fileName.tpr -ox $outName.ca.avg.pdb -oq $outName.ca.bFactor.pdb -o $outName.ca.rmsf.xvg -res`;

`echo 1 0 |g_gyrate -f $fileName.xtc -s $fileName.tpr -o $outName.prot.gyration.xvg`; `echo 3 0 |g_gyrate -f $fileName.xtc -s $fileName.tpr -o $outName.ca.gyration.xvg`;


`echo 1 | trjconv -f traj_nojump.xtc -s $fileName.tpr -o protein.xtc`; `echo 1 1 | g_rms -f protein.xtc -s $outName.prot.avg.pdb -o $outName.rmsd-all-atom-vs-average.xvg`; `echo 3 3 |g_rms -f protein.xtc -s $outName.ca.avg.pdb -o $outName.rmsd-ca-vs-average.xvg`;

`rm traj_*`;

</source>