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Article ID: 682 - Last Modified: June 7, 2011

I cannot define a core in a molecule of more than 25 atoms or so, for a Glide core constraint. I am getting the SMARTS pattern from the Workspace, but it seems that the SMARTS pattern is too long. How do I go about this?

The length limit arises only when the core molecule is specified by an explicit SMARTS pattern rather than simply using the reference structure. If you need to specify a large core that is a substructure of a reference ligand, there are two ways to work around the SMARTS pattern being too long.

First, you could get the SMARTS pattern from the Workspace selection as before, but then edit the pattern to remove some of the additional information. For example, change "[C-0X4]" to just "[C]", leaving in any non-zero formal charge specifications, though (e.g., "[N+]"). By removing the number of connections per atom, this will make your pattern a bit more general, but since it is very long, it still probably will match only the desired substructure.

Second, you could prepare a reference molecule that has just the substructure, and use that molecule as the core rather than specifying a SMARTS pattern. For this, you'll have to delete the parts of the original molecule you don't want in the pattern, and then add hydrogens. This should work as long as you're only using the heavy atoms for the core and haven't broken any double bonds or rings.

Keywords: length limit , large core, SMARTS pattern, define core, Glide

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