Article ID: 747 - Last Modified: May 16, 2011
If I were to dock a big ligand like a carbohydrate hexasaccharide, how do I increase size of the inner box?
First, note that hexasaccharide docking will be very challenging, due to the extremely large conformational space (>30 rotatable bonds).
It is possible to increase the size of the inner box beyond 14 Å by editing the jobname.in file and running the job from the command line,
The INNERBOX keyword is used to set the dimensions of the inner box. There is a hard-coded limit to the number of site points in a Glide Grid Generation job, and this effectively limits the allowed size of the inner box to roughly 22x22x22.
Also, keep in mind that the inner box usually doesn't have to be very large for an effective search. The inner box bounds the region in which the ligand center ("diameter midpoint") can be located. Since the ligand is very large, the inner box can be significantly smaller than the outer box, which bounds the region in which all ligand atoms must be located.
Keywords: Glide, hexasaccharide docking, inner box, size, large ligand
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