Article ID: 1372 - Last Modified: April 19, 2011
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.
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.
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.
- Obtain a query sequence file to test. You can use your sequence or acquire a query sequence file in FASTA format, for example:
Give the file a name, for instance query.fasta.
Create a secondary structure prediction input file
with a name such as ssp_test.inp, as follows:
# start file ssp_test.inp
# end file
Replace method with either
Run the secondary structure prediction from the
command line, with debugging.
$SCHRODINGER/ssp -WAIT -DEBUG ssp_test
Check the output files
ssp_test.log. If the prediction failed, rerun the test prediction with the
$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
ls -l $SCHRODINGER/thirdparty
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