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Article ID: 1243 - Last Modified:

What is the structure of LigPrep?

The LigPrep package consists of three components:

  1. The Maestro graphical user interface provides common access to all Schrödinger modeling technologies and is designed to allow a simple and efficient workflow.
  2. LigPrep's ligand processing software.
  3. para_ligprep, a utility program for distributing LigPrep calculations involving a number of ligands across multiple processors.

Ligand processing software consists of a set of programs bound together into a coherent package by the master LigPrep script providing a convenient way to collectively and effectively apply a number of tools to prepare ligands for subsequent processing. These tools include the utilities:

sdconvert or smiles_to_mae Convert to and from SD formatted files or from SMILES formatted files.
maesubset Select a subset of the structures from the input set.
applyhtreat Add H atoms to each CT.
desalter Remove all but the largest molecule from each CT. Intended to remove counter ions in salts.
neutralizer Neutralize charged groups if possible by adding or removing H atoms.
ionizer Generate various ionization states for the structures.
tautomerizer Generate various tautomers for the structures.
ligparse Remove structures matching specified conditions such as Molecular weight > 1000 or containing specific functional groups.
stereoizer Identify additional chiral atoms in the structures. Generates additional identical structures with different chiral properties.
ring_conf Generate one or more low energy ring conformations for each structure.
premin Separate out structures that may cause program failures in subsequent processing.
bmin Minimize structures, or if deemed necessary, automatically perform a short conformational search, to relax the structure into 3 dimensions while strongly encouraging chiral centers to adopt the chiralities indicated by the properties present for each structure.

The sdconvert, maesubset, applyhtreat, desalter, neutralizer, tautomerizer, and ionizer tools may be useful outside the LigPrep process.

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