Job control
Schrodinger Job control
Readers and Writers
Read and write structure files. Read a list of PDB files from a directory. [Requires: Maestro] See also: - Docking - Grid generation: Glide grid […]
Database preparation 1-2
Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]
MM Conformational search 1-4
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Node MSV
[Version: 2.9.0] [Requires: Maestro]
Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]
GroupBy 1-2
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
Shape screening 1-4
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
QM properties
Calculate molecular orbitals and vibrational frequencies. [Requires: Ligprep, Jaguar] [Keywords: quantum mechanics, semi-empirical, parameter flow […]