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.
If you need additional help, please email us at help@schrodinger.com.
Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles