Tutorial 5: Get A Better PDB File

In this tutorial, we will show you how to use pdbtop to convert PDB and XYZ files to a better format.

Using PSF Information

Sometimes you have an XYZ file (maybe obtained from an MD simulation) that does not have information like atom names, residue names, etc. You can use the PSF file to correct them. The following example will show you how to do that.

$ pdbtop pdb -i d5-final.xyz -t d5.psf -o d5-final

Then, in d5-final.pdb, you will see correct atom names etc. It also works for PDB files.

Wrapping Molecules into a Box

In an MD simulation with periodic boundary conditions, the coordinates of a molecule may be outside the box. You can use the following command to wrap them into a box.

$ pdbtop pdb -i d5-final.xyz -t d5.psf -o d5-pbc --box "70 70 70" # or "-i d5-final.pdb"; both work

A good point is that a residue will NOT be split into two parts. The results are shown below: