huhlim / casp13_analysis

CASP13 analysis

Prerequisite

• Python 3
• Python libraries: NumPy, MDTraj, MSMBuilder

Initial setup

• Decompress the tgz files
  tar xzf tICA_model.tgz
  tar xzf tICA_npz.tgz

Files in each directory

• scripts: scripts for the tICA analysis
• native/init: the native structures and the initial models
• example: example files
• tICA_model: pickle files for tICA models
• tICA_npz: tICA coordinates for trajectories used for the analysis described in the paper.
  You can load the npz file as follows:

  tICA_crd = np.load(npz_file, allow_pickle=True, encoding='latin1')

  There are three items in tICA_crd:
  • tICA_crd['ref_crd']: tICA coordinates for the native structure
  • tICA_crd['ini_crd']: tICA coordinates for the initial model
  • tICA_crd['tICA_crd']: tICA coordinates for the MD simulation trajectories

How to run the script

./scripts/proj_tICA.py --target TARGET --top TOPOLOGY_PDB_FILE --traj TRAJECTORY_FILEs --output OUTPUT.npy

• TARGET: one of the CASP target IDs, R0974s1, R0986s1, R0986s2, R1002-D2
• TOPOLOGY_PDB_FILE: topology file in PDB format for reading trajectory files
• TRAJECTORY_FILEs: trajectory files to get tICA coordinates. You can provide multiple files at a time.
• OUTPUT.npy: mapped tICA coordinates in a NumPy npy file.
  In the output npy file, it contains a NumPy array or a list with a length of (Number of trajectory files), and each item in the list is an array of tICA coordinates with a shape of (Number of frames, Number of tICs(=5)).

Example

In the example directory, there is an example script, run.sh, and example files.

References

• Lim Heo, Collin F. Arbour, and Michael Feig, Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations. Proteins, (2019) 87, 1263-1275 LINK