Article ID: 1243 - Last Modified: June 3, 2011
What is the structure of LigPrep?
The LigPrep package consists of three components:
- The Maestro graphical user interface provides common access to all Schrödinger modeling technologies and is designed to allow a simple and efficient workflow.
- LigPrep's ligand processing software.
- 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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