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Protein Surface Printer

A versatile program that analyzes protein surfaces from MD trajectory.

Usage:

Python /SurfacePrinter/main.py -trj TRAJ_FILE -top TOPO_FILE -ndx1 SELECTED_GROUP -ndx2 REF_GROUP -b BEGIN_TIME -e END_TIME -skip FREQUENCY

the -ndx1 & -ndx2 are strings that used to select atoms following MDAnalysis syntax https://docs.mdanalysis.org/stable/documentation_pages/selections.html

The program will analyze the surface of molecules in -ndx1 that is in contact with atoms in -ndx2.

Ex:

-ndx1 "protein" -ndx2 "water" will analyze the solvent accessible surface area of the protein in water.

For more details, please refer to the article:

J. Chem. Inf. Model. 2020, 60, 10, 5255–5264, DOI: doi.org/10.1021/acs.jcim.0c00582

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