Article ID: 856 - Last Modified: May 20, 2011
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, 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#' *.pdbHere 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.
Keywords: membrane, protein, Desmond, Prime
Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles