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Article ID: 1493 - Last Modified:

How can I run MacroModel jobs serially, one after another? I only have one MacroModel license, so I can't run them at the same time.

One way of doing this is to write a script, which can be a simple shell script (or DOS batch script on Windows) that lists the commands for the jobs you want to run. You should ensure that you use the -WAIT option to the bmin command so that each job finishes before the next job is run. For example, if you want to run three jobs sequentially, you could run the following Bash script on Linux from the directory that contained the input files for the job:

#!/bin/bash
export SCHRODINGER=install-dir
$SCHRODINGER/bmin -WAIT job1
$SCHRODINGER/bmin -WAIT job2
$SCHRODINGER/bmin -WAIT job3

On Windows, you coud create the following .bat file in the folder that contains the input, and execute it from a Schrodinger Command Prompt window.

bmin -WAIT job1
bmin -WAIT job2
bmin -WAIT job3

If you have a queueing system that supports license checking, you can submit the jobs to the queue, and the queue manager will not start a job until the required licenses are available. See Chapter 6 of the Installation Guide for information on setting up a queue with license checking.

There is also a script, $SCHRODINGER/utilities/queue_bmin that performs this task. It can run up to 12 consecutive jobs. If the job names are entered correctly, the structural output for an initial job can be used in a subsequent job. This is a C shell script, and can't be run on Windows in the Schrodinger Command Prompt Window or in the SchrodingerShell.

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