View source for 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.