Article ID: 145 - Last Modified: May 30, 2014
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 Schrödinger'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 applications for generating a suitable conformer set for use with Glide. MacroModel is generally the better choice, especially if you have large rings. ConfGen is faster and is geared towards bioactive conformations, so it would be preferred if you are screening of a large number of molecules.
The final docked results can be easily filtered using the $SCHRODINGER/utilities/glide_sort application.
#1684: Is there a way to run a conformational search specifically for macrocycles?
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