2022 AMBER tutorial 3 with PDBID 1X70

"introduction"

In this tutorial, we will be doing molecular dynamics (MD) simulations using Amber 16. This will allow us to obtain much more detailed information about the binding affinities of a ligand with a receptor. Like the DOCK tutorial, we should start with setting up the directory. This can be done with the following command.

 mkdir 001_structure 002_parameters 003_leap 004_equil 005_production

"Making the structures"

It is recommended to start fresh with the receptor and ligand files. Do the same process as in the DOCK tutorial. Start with importing pdb code 1X70, then isolate one of the proteins and its associated ligand. With an isolated protein, you can do the following command

 Select -> residue -> all nonstandard

then do

 actions -> atoms/bonds -> delete

This should isolate the protein and remove all of the nonstandard amino acids. With this, we can save this as a pdb and title it 1X70_fresh.pdb

Moving on to the ligand, we can repeat the same process as above but just isolate the ligand instead. So start with the fresh pdb code, then select the ligand and do

 Select -> Invert (selected molecules)

and

 actions -> atoms/bonds -> delete

This should isolate the ligand. Then we have to make sure it is charged properly and has hydrogens. We can do that with the following two commands.

Tools -> Structure Editing -> Add H
Tools -> Structure Editing -> Add Charge -> (have Amber ff14SB and AM1-BCC selected) -> Ok