Difference between revisions of "Gaucher Task10 Protocol"
From Bioinformatikpedia
(Created page with "== Sources == You can checkout the git repository containing all relevant data an scripts by: <pre> git clone /mnt/home/student/angermue/mp/tasks/task10 </pre> == Checking the …") |
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<pre> |
<pre> |
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gmxcheck -f traj.xtc |
gmxcheck -f traj.xtc |
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| + | </pre> |
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| + | |||
| + | == Visualizing the results == |
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| + | Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows: |
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| + | <pre> |
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| + | trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc <<EOF |
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| + | 0 |
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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> |
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| + | Next, we created a PDB file with several states using the time resolution $TIME=10: |
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| + | <pre> |
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| + | trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb <<EOF |
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| + | 1 |
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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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| + | 1 |
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| + | EOF |
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</pre> |
</pre> |
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Revision as of 20:35, 23 July 2012
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:
trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc <<EOF
0
EOF
trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc <<EOF
1
0
EOF
trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc <<EOF
1
0
EOF
Next, we created a PDB file with several states using the time resolution $TIME=10:
trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb <<EOF
1
EOF
g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME <<EOF
1
EOF
