Difference between revisions of "Gaucher Task10 Protocol"
From Bioinformatikpedia
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Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows: |
Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows: |
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<pre> |
<pre> |
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| − | trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc |
+ | echo 0 | trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc |
| + | echo 1 0 | trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc |
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| − | 0 |
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| + | echo 1 0 | trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc |
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| − | EOF |
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| − | trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc <<EOF |
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| − | 1 |
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| − | 0 |
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| − | EOF |
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| − | trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc <<EOF |
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| − | 1 |
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| − | 0 |
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| − | EOF |
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</pre> |
</pre> |
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Next, we created a PDB file with several states using the time resolution $TIME=10: |
Next, we created a PDB file with several states using the time resolution $TIME=10: |
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<pre> |
<pre> |
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| − | trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb |
+ | echo 1 |trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb |
| + | echo 1 | g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME |
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| − | 1 |
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| + | </pre> |
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| − | EOF |
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| + | |||
| − | g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME <<EOF |
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| + | == Quality assurance == |
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| − | 1 |
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| + | === Thermodynamic parameters === |
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| − | EOF |
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| + | <pre> |
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| + | echo "12 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_temp.xvg > $A/${NAME}_temp.out |
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| + | echo "13 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pres.xvg > $A/${NAME}_pres.out |
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| + | echo "11 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_tot.xvg > $A/${NAME}_tot.out |
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| + | echo "9 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pot.xvg > $A/${NAME}_pot.out |
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| + | </pre> |
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| + | |||
| + | === Root Mean Square Deviation === |
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| + | <pre> |
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| + | echo 1 1 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p_start.xvg |
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| + | echo 4 4 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b_start.xvg |
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| + | echo 1 1 | g_rms -f ${MB}_norot.xtc -s ${A}/${NAME}_rmsf_p_avg.pdb -o ${AB}_p_avg.xvg |
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| + | echo 4 | g_rmsdist -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b.xvg |
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| + | </pre> |
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| + | |||
| + | === Radius of gyration === |
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| + | <pre> |
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| + | echo 1 | g_gyrate -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg |
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| + | </pre> |
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| + | |||
| + | === Minimum distance between periodic boundary cells === |
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| + | <pre> |
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| + | echo 1 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_p.xvg -pi > $A/${NAME}_mindist_p.out |
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| + | echo 3 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_c.xvg -pi > $A/${NAME}_mindist_c.out |
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| + | </pre> |
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| + | |||
| + | == RMSF == |
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| + | <pre> |
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| + | echo 3 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_c.xvg -ox ${AB}_c_avg.pdb -oq ${AB}_c_bfac.pdb -res > ${AB}_c.out |
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| + | echo 1 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p.xvg -ox ${AB}_p_avg.pdb -oq ${AB}_p_bfac.pdb -res > ${AB}_p.out |
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| + | </pre> |
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| + | |||
| + | == Hydrogen bond network == |
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| + | <pre> |
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| + | echo 1 1 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pp.xvg |
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| + | echo 1 12 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pw.xvg |
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| + | </pre> |
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| + | |||
| + | == Solvent Accessibility Surface == |
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| + | <pre> |
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| + | echo 1 1 | g_sas -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_all.xvg -or ${AB}_res.xvg -oa ${AB}_at.xvg |
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| + | </pre> |
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| + | |||
| + | == Ramachandran plot == |
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| + | <pre> |
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| + | g_rama -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg |
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| + | </pre> |
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| + | |||
| + | == Analysis of dynamics and time-averaged properties == |
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| + | <pre> |
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| + | echo 6 6 | g_cluster -s $MB.tpr -f ${MB}_norot.xtc -dm $A/${NAME}_rms.xpm -dist ${AB}_distrib.xvg \ |
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| + | -o ${AB}_clusters.xpm -sz ${AB}_sizes.xvg -tr ${AB}_transbox.xpm -ntr ${AB}_trans.xvg \ |
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| + | -clid ${AB}_time.xvg -cl ${AB}_clusters.pdb -cutoff $C -method gromos -dt 10 -minstruct 50 |
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</pre> |
</pre> |
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Latest revision as of 05:51, 13 August 2012
Contents
Sources
You can checkout the git repository containing all relevant data an scripts by:
git clone /mnt/home/student/angermue/mp/tasks/task10
Checking the results
gmxcheck -f traj.xtc
Visualizing the results
Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows:
echo 0 | trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc
echo 1 0 | trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc
echo 1 0 | trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc
Next, we created a PDB file with several states using the time resolution $TIME=10:
echo 1 |trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb
echo 1 | g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME
Quality assurance
Thermodynamic parameters
echo "12 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_temp.xvg > $A/${NAME}_temp.out
echo "13 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pres.xvg > $A/${NAME}_pres.out
echo "11 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_tot.xvg > $A/${NAME}_tot.out
echo "9 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pot.xvg > $A/${NAME}_pot.out
Root Mean Square Deviation
echo 1 1 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p_start.xvg
echo 4 4 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b_start.xvg
echo 1 1 | g_rms -f ${MB}_norot.xtc -s ${A}/${NAME}_rmsf_p_avg.pdb -o ${AB}_p_avg.xvg
echo 4 | g_rmsdist -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b.xvg
Radius of gyration
echo 1 | g_gyrate -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg
Minimum distance between periodic boundary cells
echo 1 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_p.xvg -pi > $A/${NAME}_mindist_p.out
echo 3 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_c.xvg -pi > $A/${NAME}_mindist_c.out
RMSF
echo 3 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_c.xvg -ox ${AB}_c_avg.pdb -oq ${AB}_c_bfac.pdb -res > ${AB}_c.out
echo 1 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p.xvg -ox ${AB}_p_avg.pdb -oq ${AB}_p_bfac.pdb -res > ${AB}_p.out
Hydrogen bond network
echo 1 1 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pp.xvg
echo 1 12 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pw.xvg
Solvent Accessibility Surface
echo 1 1 | g_sas -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_all.xvg -or ${AB}_res.xvg -oa ${AB}_at.xvg
Ramachandran plot
g_rama -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg
Analysis of dynamics and time-averaged properties
echo 6 6 | g_cluster -s $MB.tpr -f ${MB}_norot.xtc -dm $A/${NAME}_rms.xpm -dist ${AB}_distrib.xvg \
-o ${AB}_clusters.xpm -sz ${AB}_sizes.xvg -tr ${AB}_transbox.xpm -ntr ${AB}_trans.xvg \
-clid ${AB}_time.xvg -cl ${AB}_clusters.pdb -cutoff $C -method gromos -dt 10 -minstruct 50
