Python script to calculate the contact surface area between two molecular structures, e.g. ligand-protein, protein-protein, among others, in a Molecular Dynamics trajectory.
It allows to carry out the analysis in the different formats supported by PyMOL, e.g., .pdb, .gro, .cms and trajectory files; .dcd, .crd, .xtc, and .trr.
It allows obtaining in a .dat file the surface area obtained by SASA of the ligand, protein, the complex, the contact area and the percentage (portion) of the ligand that makes the contact.
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Python
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PyMOL libraries
To install PyMOL libraries by console use:
sudo apt-get install pymol
python md_contact_surface.py -top topology_file.xxx -traj trajectory_file.xxx -l "ligand_selection" -p "protein_selection" -o contact_surface_data
It is also possible to specify the frames of the trajectory to be analyzed. The initial and final frame can be specified as: -f 1:1000, this option will analyze each frame from position 1 to 1000. But also the spacing between frames can be specified, for example the option: -f 1:1000:5 will consider every 5 frames in the range 1 - 1000.
To see available options use:
python md_contact_surface.py -h
Be sure to thank these contributors:
- Mauricio Bedoya - Creator, maintainer
- Francisco Adasme - Contributor
Licensed under the MIT license, see the separate LICENSE file.
- Mauricio Bedoya, & Francisco Adasme. (2020, October 14). Contact surface analyzer: v1.0 (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.4088995
- PyMOL
