Simple scripts for LEaP to create topology and coordinate files

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 (you do not have to forward X session when connect with other computer).

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

On the beginning LEaP is reading force field parameters and AMBER libraries, then 8 Alanine peptide is built, 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. Protein is built as extended chain therefore it is recommended to minimize it before any analysis.

2. You have PDB file containing residues defined in AMBER libraries (amino acid and nucleic residues, some ions and solvent molecules; see $AMBERHOME/dat/leap/lib directory), let us assume that it is called my_protein.pdb:

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

NOTE: Remove all hydrogens belonging to amino acid and nucleic residues, LEaP will add them according to AMBER libraries. In case of wrong atom names or atoms types or residue names, you will find appropriate warnings in leap.log file which is output file from LEaP.

3. As above but this time PDB contains some residue (e.g. ligand) which is not defined in AMBER libraries and there is no ready force field parameters for it. Let us assume that ligand residue is called LIG in PDB file.

 source leaprc.ff03
 source leaprc.gaff
 loadamberprep LIG.prepin
 loadamberparams LIG.frcmod
 mol=loadpdb my_protein.pdb
 saveamberparm mol my_protein.top my_protein.cord
 savepdb mol my_protein_out.pdb
 quit

As you can see above, you need two additional files with force field parameters for that ligand: LIG.frcmod and LIG.prepin. Information how to get them you can find in two tutorials: Generating parameters using AMBER's built in General Forcefield (gaff) and Preparing an AMBER topology file for a protein plus ligand system. If you have more than one new residue, just load frcmod and prepin files for each of them.