Article ID: 145 - Last Modified: December 4, 2010
Do I need to generate multiple conformations of my ligands to run Glide?
You will need to supply Glide with at least one reasonable three-dimensional structure in order to obtain good results. Given this single structure Glide's internal conformation generator (based on Schrodinger's ConfGen package) will be sufficient to dock many molecules accurately and in a timely manner.
There may however be occasions when it is sensible to augment Glide's internal conformational search routines (for example when docking particularly flexible molecules, when docking to a tight active site, or when using core constraints) with some additional conformers. ConfGen or MacroModel are probably the best methods of generating a suitable conformer library for use with Glide.
The final docked results can be easily filtered using the $SCHRODINGER/utilities/glide_sort application.
Keywords: ConfGen, Glide, LigPrep
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