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Secondary Structure using DSSP
The code is adopted and changed from the following script for secondary structure calculation in VMD. https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/
This analysis computes the secondary structure of protein residues in time for a dcd trajectory. The scripts needed can be downloaded from below.
Steps
1) change the psf and dcd in ss_content.tcl according to where these files are in your directory 2) change the last_file number in ss_content.csh according to the number of trajectories. If you are using a supercomputer other than deepthought2 change this file accordingly. 3) run ss_content.csh ( sbatch ss_content.csh) 4) this will give you multiple .dat files containing the secondary structure in each trajectory. you can combine these into a single secondary_structure file for further analysis.
This can be done by the following code:
for i in {1..40};do sed '1~10!d' sec_structure-$i.dat » ss_content.dat done