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Article ID: 856 - Last Modified:

Can I use proteins from the OPM database to define membranes for these proteins in Desmond or Prime?

Yes, you can use these proteins. However, prior to 2013, some of these proteins have incorrectly formatted REMARK records, in which the text starts in column 9 instead of column 12, and must be fixed before you can use them. To fix them, you can use the command:

perl -pi -e 's#REMARK  1/2#REMARK     1/2#' *.pdb

Here there are two spaces after the first REMARK and five after the second.

When the file is converted by pdbconvert or imported into Maestro, it should have the property "OPM membrane thickness" r_pdb_OPM_membrane_thickness). If it does not, check that these REMARK records are properly formatted.

The OPM database has been updated to comply with the formatting standard. If you have older versions of files from the OPM database, you should replace them with the newer, fixed versions.

Keywords: membrane, protein, Desmond, Prime

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#243: What is the best way to place a membrane for my GPCR model to use in Desmond?

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