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A particular sequence gave the following error when I tried to run SSpro locally:

ERROR: query sequence in alignment different from query sequence given on cmdline
ERROR: unable to pad alignment
ERROR: unable to convert Blast output to SSpro format
ERROR: parsing blast output

Any idea what the problem might be?

We have seen this only on a couple of occasions, and it could have to do with SSPro not finding any hits (e.g., it could happen for a short sequence).

You can try to set the following environment variable to use the much large 'nr' sequence database rather than the default 'pdb' (however, note, that SSpro will now take much longer to run because it has to run BLAST against the nr database):
for bash: export PSP_SSPRO_DB = nr
for t/csh: setenv PSP_SSPRO_DB nr

After setting this environment variable, start up Maestro from the shell where the environment variable was set and try the job again.

We have also in the past seen this problem when older versions of BLAST have been used with newer versions of Prime.

Keywords: Prime, side-chain prediction, SSpro

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