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Article ID: 703 - Last Modified: May 16, 2011

Is there a way to define constraints such as H-bonds for a Glide command line run, other than using atom numbers?

H-bond constraints must be specified by receptor atom number. If you don't want to set up these Grid Generation jobs in Maestro, you could try using a Python script to generate the input files. The Schr&puml;dinger Python API provides classes for writing Grid Generation and Ligand Docking input files, and to find the atom number for the receptor atom based on an ASL expression.

Keywords: constraints, Glide, command line

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