Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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Chapter 10: <strong>Prime</strong> MM-GBSA<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong><br />
Figure 10.1. The <strong>Prime</strong> MM-GBSA panel.<br />
4. Click Start to start the job, or click Write to write the input file and run the job from the<br />
command line.<br />
When you click Start, the Start dialog box opens, in which you can choose to incorporate<br />
the results into the Maestro project, set the job name, select the host, and set the number<br />
of CPUS and number of subjobs, if you are running the job on a multiprocessor host or<br />
submitting it to a queuing system. You can divide the ligand set between a specified number<br />
of subjobs, to achieve load balancing. The number of subjobs must be no smaller than<br />
the number of CPUs, and for optimal load balancing, should be several times the number<br />
of CPUs.<br />
You can also run <strong>Prime</strong> MM-GBSA from the command line on Unix, with the input file written<br />
from the panel. The syntax is as follows:<br />
$SCHRODINGER/prime_mmgbsa [options] input-file<br />
The input file must be a Maestro file with the receptor as the first entry followed by one or<br />
more ligands (i.e. pose viewer file format). The options are described in Table 10.1.
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