In this tutorial, the radii calculations of nanotube and protein are introduced. This tutorial is divided into three parts: nanotube radii calculation, protein radii calculation and advance radii calculation in peptide channel. The advance radii calculation is based on the PDB and PSF files which are produced by the CHARMM force field. Here, MolAICal (https://doi.org/10.1093/bib/bbaa161) is employed for this tutorial.
2. Materials
2.1. Software requirement
1) MolAICal: https://molaical.github.io
2) VMD: https://www.ks.uiuc.edu/Research/vmd
2.2. Example files
1) All the necessary tutorial files are downloaded from:
https://github.com/MolAICal/tutorials/tree/master/005-radiiCal
For more detailed procedures, please go to https://molaical.github.io, and click the section named "Tutorials" in the left part of webpage. Once "Tutorials" open, you can freely find pdf file about this tutorial (see Figure 1):
Figure 1
You can repeat this tutorial according to the content of pdf file.
