Article ID: 859 - Last Modified: May 20, 2011
I ran a Glide docking job with constraints, but the job failed with the error "unable to allocate floats". What can I do about this?
Docking jobs with receptor-based constraints can fail due to insufficient memory, if the constraint specification allows too many different combinations of ligand atoms to satisfy it. Some workarounds are:
- Reduce the number of ways of satisfying constraints. For example, requiring 4 constraints out of 10 be satisfied (the maximum allowed for both numbers) results in 210 ways of satisfying the constraints, whereas requiring 4 constraints out of 8 to be satisfied results in 70 ways, requiring 3 constraints out of 10 results in 120 ways, and requiring 4 out of 4 results in only 1 way.
- Use SMARTS patterns that are more specific, to reduce the number of atoms that match. For example, [*], which matches any atom, and [#6], which matches any carbon atom, are probably too general.
- Use a machine with more memory.
Keywords: Glide, constraints, error
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