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Leap – Chemistry Through a Computational Lens
Fundamentals of LEaP By Pengfei Li and David Cerutti Background Information The LEaP program is a portal between many chemical structure file types ( .pdb and .mol2, primarily), and the Amber model parameter file types such as .lib, .prepi, parm.dat, and .frcmod). Each of the parameter files contains pieces of information needed for constructing a simulation, whether for energy minimization or molecular dynamics.
In Amber16 and later versions, we have defined leaprc files for different descriptions of proteins, nucleic acids, and solvents (including a number of water models), so that you can mix and match as you need. The antechamber program will generate its own.frcmod files for custom-built residues, typically using the General Amber Force Field, but the exact source of parameters is subject to some user control. If the disulfide bridge is lost, the CYS residues will not be correctly converted to CYX and instead reduced (hydrogen added to the thiol) in the simulation.
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