Prime User Manual - ISP

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Chapter 9: Docking Covalently Bound Ligands
You can extend your selection to include residues that are within a given distance of the
selected residues. To do so, enter a value in the Include residues within N Å of picked residues
text box. These residues are also added to the list in the Additional residues text box.
You can remove residues from the list to sample by deleting them from the Additional residues
text box.
9.1.5 Running the Job
When you have finished making settings, click Start to open the Start dialog box. In this dialog
box you can make job settings and start the job.
The results are returned in a Maestro file. Each pose includes both the ligand and the receptor,
one pose for each ligand attachment point found.
9.2 Running Covalent Docking from the Command Line
It is also possible to run covalent docking jobs from the command line. To do so, you should
first set up the input file in the Covalent Docking panel, as described in the previous section,
and then click Write, to write the input file for the job. This button opens a file selector, in
which you can browse to the location and choose the file name.
The covalent docking job is run with the same pipelining workflow scripts as other workflows,
such as the Virtual Screening Workflow (VSW) and Quantum-Polarized Ligand Docking
(QPLD). Covalent docking does not have its own script, so you can use the script for VSW, and
run the job as
$SCHRODINGER/vsw [job-options] input-file
The job options are the usual Job Control options that specify the host and other resources.
These options are described in Section 2.3 of the Job Control Guide.
Prime 2.1 User Manual