Knowledge Base

To design and use a custom reaction type in your covalent docking run, you can use a set of keywords that specify the receptor reaction site, the ligand reaction site, and the changes in bonding, charge, or chirality that take place in the reaction. These keywords can be added to the input file (jobname.inp) if you want to run the job from the command line. They can also be saved in a custom chemistry file, my-reaction.cdock, and then selected in the Covalent Docking panel by choosing Custom for the reaction type and browsing to the file.

See Custom Chemistry Definitions for Covalent Docking in the Covalent Docking Command Reference for details of setting up the custom chemistry and using it.  This section includes an example of a custom chemistry file as well as a description of the syntax.

Custom chemistry settings for all of the built-in reactions can be printed with the command:

$SCHRODINGER/covalent_docking -print_named_reactions

You can download additional custom reaction types from the Covalent Reactions Repository.  my-reaction.cdock files for the built-in reactions also are available in this repository.