Weird message whenever I try to calculate energies

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    • August 20, 2010 at 12:55 pm #656
      Anonymous

        Hi All,

        I’ve just managed to get PyRosetta running on my system. Everything seems to work fine, but I get this message whenever I try to calculate energies, or use any sort of scoring functions.

        Warning: Unable to locate database file Dunbrack02.lib.bin

        core.scoring.dunbrack: Dunbrack library took 1.99 seconds to load from ASCII

        Warning: Unable to locate database file Dunbrack02.lib.bin

        Warning: Unable to locate database file Dunbrack02.lib.bin

        core.scoring.dunbrack: Opening file

        /struct/software/linux/pyrosetta-1.1/minirosetta_database/dun02F2R5X9 for output.

        core.scoring.dunbrack: Unable to open temporary file in rosetta database for writing the

        binary version of the Dunbrack02 library.

        Does this mean all my calculations will be slower than if I have the correct database file? Does anyone else seen this message? It is slightly weird since even after this message, the program seems to calculate some sort of energy and gives an output. I just hope it’s the correct output!

        Any comments will be most welcome, and highly appreciated.

        With best wishes

        Thanks to all for reading

        T.

      • August 23, 2010 at 2:51 pm #4584
        Anonymous

          This is a core Rosetta issue, not a PyRosetta issue. I think.

          The Dunbrack library is a huge flat file in human-readable format. For speed, the library-reading machinery attempts to serialize it and store it on disk in a binary format (Dunbrack##.lib.bin). This serialized binary format is not portable from computer to computer, but reads in to memory two orders of magnitude faster than the flat file does.

          These repeated error messages probably mean that you (or your Pyrosetta process) do not have write access to the rosetta_database directory.

          I don’t think it will harm you in the long run other than being slow. You should check that packing in general, and your Dunbrack scores in your scorefunction, are working right.

        • September 9, 2010 at 5:43 pm #4612
          Anonymous

            Thanks a lot!

            The packing of the proteins seems to be fine. I think it is just a slowing down issue then. I certainly don’t have write access to the rosetta directory. It must be the reason.

            Thanks again…..

            > Hi All,
            >
            > I’ve just managed to get PyRosetta running on my system. Everything seems to work fine, but I get this message whenever I try to calculate energies, or use any sort of scoring functions.
            >

            > Warning: Unable to locate database file Dunbrack02.lib.bin
            >
            > core.scoring.dunbrack: Dunbrack library took 1.99 seconds to load from ASCII
            >
            > Warning: Unable to locate database file Dunbrack02.lib.bin
            >
            > Warning: Unable to locate database file Dunbrack02.lib.bin
            >
            > core.scoring.dunbrack: Opening file
            >
            > /struct/software/linux/pyrosetta-1.1/minirosetta_database/dun02F2R5X9 for output.
            >
            > core.scoring.dunbrack: Unable to open temporary file in rosetta database for writing the
            >
            > binary version of the Dunbrack02 library.
            >

            > Does this mean all my calculations will be slower than if I have the correct database file? Does anyone else seen this message? It is slightly weird since even after this message, the program seems to calculate some sort of energy and gives an output. I just hope it’s the correct output!
            >
            > Any comments will be most welcome, and highly appreciated.
            >
            > With best wishes
            >
            > Thanks to all for reading
            >
            > T.

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