I have used modeller to generate a pdb file. i have run it on PROCHECK. but the input format is not compatible. (brook haven format). How do i convert my file? or any other way? Please help. ASAP
PROCHECK already accepts .pdb files. As far as I understand, Brookhaven might be an alternative way to call the PDB format (an old one, maybe?). I found some references to it around the internet, e.g. "Brookhaven Protein Databank format".
Anyway, just a remark: check to see if protein chains are specified in the MODELLER output file (sometimes MODELLER doesn't set chain IDs; this can cause problems with PROCHECK). If in doubt, don't use the chain parameter in the PROCHECK command, e.g. `procheck model.B99990004.pdb 2.0`. The resolution parameter is necessary, but any number is accepted (I've used 2.0 in the example above).
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