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.

1. You need to build a peptide from a sequence:

 source leaprc.ff03
 mol = sequence {NALA ALA ALA ALA ALA ALA ALA CALA}
 saveamberparm mol mol.prmtop mol.inpcrd
 savepdb mol mol.pdb
 quit

or you can build a protein from an existing pdb file. There are two energy function that are most likely to be used an ALL-ATOM model or an UNITED ATOM model. For the ALL-ATOM model source leaprc.ff03 or an UNITED ATOM model source leaprc.ff03ua

     source leaprc.ff03
     mol=loadpdb protein.pdb.
     saveamberparm mol mol.prmtop  mol.inpcrd
     savepdb mol mol.pdb              
     quit                                               

On the beginning LEaP is reading force field parameters and AMBER libraries, and finally three files are produced: mol.prmtop with topology, mol.inpcrd with coordinates and mol.pdb which is PDB file that you can use to visualize the protein.