First things first: the AMBER LEaP tutorial is incredibly explanative. LEaP, in the forms tleap or xleap is used to generate AMBER systems.

Table: Commands in the LEaP syntax

Command Objective Example Ex. Explanation
source load in force field parameters source leaprc.ff14SB loads in the ff14SB force field
loadpdb load in a PDB file loadpdb foo system.pdb loads in the PDB, all future references are to foo
loadmol2 load in a mol2 file res = loadmol2 residue123.mol2 loads in the topology and charge information for non-standard residue, all future references are to res
loadamberprep load in a prepi file for a non-standard residue loadamberprep residue234.prepi loads in the topology information for the non-standard residue file residue234.prepi
loadamberparams load in an frcmod file for a non-standard residue loadamberparams residue234.frcmod load in the force field information for the non-standard residue file residue234.prepi
check make sure that there aren’t errors check foo checks the loaded foo for errors
select choose specific atoms for the Unit editor select foo.135 selects residue 135 of foo
edit opens the selection in the Unit editor edit foo opens foo the Unit editor; any selected residues will the be highlighted
solvateoct solvate the system as a truncated octahedron solvateoct foo TIP3P 12.00 solvates the loaded foo with TIP3P water extending at least 12.00 Å from the protein’s surface
solvatebox solvate the system as a square box solvatebox foo TIP3P 12.00 solvates the loaded foo with TIP3P water extending at least 12.00 Å from the protein’s surface
addions add ions to neutralize the system (commonly K+, Na+, or Cl-) addions foo K+ 0 neutralizes foo with potassium ions to a net charge of 0
saveamberprep saves a prepi file saveamberprep R234 res234-fix.prepi saves a new prepi file, which means that fixed systems can be rebuilt with the modified prepi
saveamberparm save the parameter and topology file saveamberparm foo system_wat.prmtop system_wat.inpcrd saves the parameter and topology files for foo that will be used for simulation
savepdb saves a PDB file savepdb foo system.pdb saves the PDB file for foo system that can serve as an informative reference
quit exit out of the program quit you guessed it… it quits

With LEaP, there are several solvent shapes to pick from. We commonly use periodic solvent boxes, which are generated using either solvateOct or solvateBox (both shown in the figure below). solvateOct solvates the system in a truncated octahedron and solvateBox solvates the system in a cuboid box. The solvateOct command makes space-filling spherical shape. This reduces solute rotation and often results in smaller systems. Having a smaller system can save time in simulations. Occasionally solvateOct has issues with centering itself correctly, but those are few and far between. Choose the solvation command you want and be consistent across that project. Additional details on these commands can be found on page 232 of the Amber18 Manual.

Shapes of box and truncated octahedron water boxes.
The different types of periodic solvent boxes for explicit solvent, solvateBox (left) and solvateOct (right).