HYDROID

ExampleMD: calculating H-SASA profiles from molecular dynamics trajectories

This additional example provides sample scripts for computing H-SASA profiles from a molecular dynamics (MD) trajectory. System: 601TA centromeric nucleosomes of S. cerevisiae (same as in example1).

• H-SASA_from_MDtrj.vmdpy does H-SASA calculations from a DCD trajectory generated by NAMD for . This python script should be run from within VMD.
• H-SASA_from_MDtrj_plot.py plots the results.
• dcd2pdb.vmdpy - extracts DCD trajectory to a set of PDB-files (required by the next script). This python script should be run from within VMD
• H-SASA_params_scan.py - calculates H-SASA profiles averaged over MD trajectory with a comprehensive set of different parameters. The results are used in ../example1/H-SASA_params.md

This site is open source. Improve this page.