Constructing a lattice: You'll need some more tools for this!

The input files that will be needed for this tutorial are available in this archive. Download the archive and put it in a suitable space, then unpack it:

[user]$ gunzip XtalUtilities.tar.gz
[user]$ tar -xvf XtalUtilities.tar

Unpacking the archive will create a directory called XtallUtilities/, wherein this tutorial will be conducted. Enter XtalUtilities:

[user]$ cd XtalUtilities
[user]$ ls

c1AHO.pdb           
Acetate.pdb      Acetate.prp         XtalSetup.sh
Ammonium.frcmod  Ammonium.pdb        leaprc.ff99SB_spce
spce.pdb         Ammonium.prp        

The relevant programs that must be available from the AmberTools15 installation in ${AMBERHOME}/bin/ include AddToBox, ChBox, CheckMD, PropPDB, and UnitCell. All of these programs take command line inputs, and also print lists of available input options if run with no arguments. Once the programs are installed, all the tools are ready for constructing crystal lattices for simulations.

Proceed to the next section.

Return to the beginning of the tutorial.