In the Prime Comparative Modeling workflow, Edit Alignment stage, the secondary structure prediction fails. What should I do?

First, check that you have the third-party software and databases properly installed — see the the Installation Guide for more information.

1. Check that the special Schrödinger and Prime environment variables are set with the commands:
   
   env | grep SCHRODINGER
env | grep PSP

   Compare the results with the environment variables listed in the Installation Guide.
2. Check that PsiPred is properly installed (Linux only). The following command should list the files in the installation. If the directory is missing, or there are no files in these directories, or if some files are missing, you will need to reinstall PsiPred.
   
   ls -l $SCHRODINGER/thirdparty/bin/platform/psipred/bin
ls -l $SCHRODINGER/thirdparty/bin/platform/psipred/data


Next, check whether you are running out of memory during the secondary structure prediction: these calculations can be memory-intensive. Perform the prediction again, and run the command top. Watch the output from top for a while to see if memory limitation is a problem.

Finally, run a sample secondary structure prediction with debugging turned on.

1. Obtain a query sequence file to test. You can use your sequence or acquire a query sequence file in FASTA format, for example:
   
   > query
AAEEKTEFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK

   Give the file a name, for instance query.fasta.
2. Create a secondary structure prediction input file with a name such as ssp_test.inp, as follows:
   
   # start file ssp_test.inp
QUERY_FILE query.fasta
METHOD method
# end file

   Replace method with either sspro or psipred.
3. Run the secondary structure prediction from the command line, with debugging.
   
   $SCHRODINGER/ssp -WAIT -DEBUG ssp_test

4. Check the output files ssp_test.out and ssp_test.log. If the prediction failed, rerun the test prediction with the -LOCAL flag:
   
   $SCHRODINGER/ssp -WAIT -DEBUG -LOCAL ssptest


Please send us all job files, including output files, if you need assistance with the analysis, along with output from the commands at the beginning of this FAQ and the following commands:

whoami; hostname; pwd; uname -a
echo $SCHRODINGER
ls -l $SCHRODINGER/thirdparty


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