I chose to do web-based homology searching with Prime, and can find homologs for my query, but I get an error when trying to run the alignment job. The error is:

WARNING Errors occurred while incorporating Calculate Alignment job jobname; job record for JobID will be removed, but not the job input and output files.

What is the problem?

Most likely, the third-party software has not been installed. From Suite 2011 on, the default installation allows you to perform homology modeling with web-based searching, so you are unlikely to encounter this problem.

In Suite 2010, even if you use the web-based searching, there are still some components that will have to be installed in order to run the alignment job. If you are using the web-based search, you will have to download and install the thirdparty software available here:

Linux platform:
ftp://ftp.schrodinger.com/support/hidden/prime/Suite2010_webbased/Linux/

Windows platform:
ftp://ftp.schrodinger.com/support/hidden/prime/Suite2010_webbased/Windows/

Please see the Installation Guide (available from Maestro: Help → Manuals Index) for more information.

Keywords: alignment error, web-based search, Prime, structure prediction, BLAST

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