Tutorial 4: Modifications and Mutations

In this tutorial, we will show you how to use pdbtop to modifications or mutations.

Before any mutations or modifications, you have to have 2 files: pdb and psf. So, please read Tutorial 1: A Standard Protein first.

Hint

For all supported modifications, please refer to the modify page.

Modifications

Assume we have a protein structure 5vbm-4.pdb and its topology 5vbm-4.psf (see Tutorial 1: A Standard Protein), and we want to perform an “asymmetric dimethylation” for the residue Arg41 at chain A, then we can use the following command:

$ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-arg41 --adma 41A

Now we check the result:

_images/p12.png

Mutations

To mutate, say, Arg41 to Serine, we can use the following command:

$ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-a41s --mutate "41A SER"

Now we check the result:

_images/p11.png

You can do multiple mutations at once, like:

$ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-6 --mutate "41A SER 45A ALA"