Prime User Manual - ISP

96
Chapter 11: Command Syntax
Files
In addition to the jobname.log and jobname.err files, multirefine produces the following
output files:
jobname-out.mae Final structures, all in a single file.
jobname.pdb PDB format file corresponding to lowest-energy structure.
Other structures will have corresponding files jobname-
2.pdb, and so on.
jobname.restart Contains information that allows a job to be restarted if it
fails.
jobname-run-N.archive.zip Archives of subjob output files.
Temporary files, which are normally deleted when no longer needed unless the debugging
option is used, are named according to the following patterns:
jobname-conf-N.* Files associated with temporary structures. All active structures in the
ensemble have a unique serial number N.
jobname-run-N.* Files associated with a given subjob. All subjobs have a unique serial
number N.
Return Value and Errors
multirefine returns a value of 0 on successful completion, 1 otherwise. All scripts run by
multirefine that return a value of 1 also print a message to the file jobname.err. This file is
empty otherwise, as all non-fatal messages are printed to the file jobname.log. Output from
Job Control goes to standard output, and any errors arising before the driver script has started
likewise go to standard output or standard error.
Restarting an Incomplete Job
If a job fails, you can restart it by submitting it again from the same directory. The
jobname.restart file and the archives of subjobs must be present in the directory, and the
directory must be accessible from the host on which the driver job runs. Also, the job records
for the failed jobs must not be purged from the job database, so that the restart mechanism has
access to information on the failed subjobs. If the job records are missing, the subjobs are
repeated.
Failed jobs that were started from Maestro must be restarted from the command line. You can
use the -PROJ and -DISP options to assign the job to the Maestro project and set the incorporation
mode.
Once the job finishes successfully, the subjob archives and the restart file are removed.
Prime 2.1 User Manual