Step 1: Download Files


In the first step, we are going to calculate the MM and QM/MM energies of the two side-chains. First, download all of the files you will need for the practical. You need to download the file called “qmmm.tar.bz2”. Click on this file, and then click on the “Download” icon at the top of the page (it is the downward pointing arrow in the center at the top of the page). Once you have downloaded the file, unpack it and then change into the qmmm directory;

tar -jxvf qmmm.tar.bz2

cd qmmm

In this directory, you should find PDB files for the two sidechains (PHE.pdb and TRP.pdb). Use VMD to look at these two files. You should see that the sidechains are methylated (have a -CH3 group attached) and are thus really the molecules toluene and 3-methylindole.

Also in this directory you should find the Amber-format topology and coordinate files for the solvated sidechains ( / PHE.crd and / TRP.crd). If you are interested and want to know how these files were created, then please click here.

Otherwise, please continue to the next stage of the practical.