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AverageHydrogenBondsAveraging hydrogen bonds across the trajectory is a useful summary measure of interactions between mRNA and the CAR/A-site anticodon. It can also be used to identify a pattern of used H-bond donors and acceptors characteristic of the experimental construct. Because this is an average measure, it should only be run on the segment of the trajectory that has been equilibrated (as determined by RMSD). Work Flow Step 1 The first step is to calculate the hydrogen bond averages. Run /mindstore/home33ext/kscopino/BIN/make_cpptraj_5a_avgHbond.py to create the cpptraj input files for each run (cpptraj_5a_avgHbond.in) and the shell script to submit cpptraj jobs to the scheduler (run_cpptraj_5a_avgHbond.sh). Then submit run_cpptraj_5a_avgHbond.sh. The output will be 16 files containing the atoms involved in hydrogen bonding during the trajectory and the frequency of those bonds. Step 2 Because each experimental trajectory can have many combinations of H-bond donors and acceptors, it is helpful to summarize across all experiments rather than examining each file individually. Run the tabulation script /mindstore/home33ext/kscopino/BIN/make_cpptraj_5b_tables.py to create a summary table of this data. The output can be directed into a file for import into Excel (python make_cpptraj_5b_table.py > output.txt). The -1,0,+1 summary lines can be used to represent the overall amount of hydrogen bonding for each construct and the individual lines can be used to create interaction maps (fig 6c and fig6ab of Scopino et al. 2020, respectively). |