Preparing an AMBER topology file for a protein system

When you want to use AMBER, either on its own to run MD, or interfaced with any of the group software (GMIN, OPTIM or PATHSAMPLE), you need to have two files at your disposal. These are the topology file (which describes the atom types, connectivity of atoms, force field parameters for angles, etc.) and the coordinate file (which shockingly defines the coordinates of the atoms in your system).

To start work with AMBER you need files defining your system (topology and coordinates) and driving file with keyword defining conditions for molecular dynamics. The detailed tutorial referring specially to point 3 (how to get the topology and coordinate files for system with ligand) is presented in tutorial Preparing an AMBER topology file for a protein plus ligand system.

Below you can find simple LEaP scripts generating topology and coordinate files for three exemplary cases. In each case you need to run ONE of the following commands:

 xleap -f leap.in
 xleap < leap.in
 tleap -f leap.in
 tleap < leap.in

where leap.in is a name of the script.

xleap is a graphical version of tleap therefore sometimes is easier to call tleap in the form of a script.