How do I prepare PDB files from the RCSB database for use with Glide?
Protein preparation involves removing unneeded molecules (e.g., waters, other subunits); correcting charges and bond orders in metal ions, ligands, cofactors, and modified residues; reorienting certain functional groups, and running a restrained minimization. These tasks can all be run using the Protein Preparation Wizard, which is available from Maestro with Schrödinger Suite 2007. Once you have run the Protein Preparation Wizard, you should check your structures carefully for any remaining problems. Detailed instructions for preparing PDB files for use with Glide and other products can be found in the Protein Preparation Guide, which is included with the general documentation. This document describes both the Protein Preparation Wizard and manual protein preparation. Some information specific to Glide is available in the Glide User Manual.
