flexpep docking problem—–How to do with phosphorylation peptide?

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    • June 2, 2011 at 7:37 am #928
      Anonymous

        Hi,everyone,
        I’m new to rosetta peptide docking. Currently, I want to dock a peptide into protein using Flexpep docking. But there is a phosphorylation in my peptide and when I use “-remember_unrecognized_res” flags, after docking the peptide is discontinuous at the phosphorylation site. Anyone knows how to solve this problem?
        Thanks in advance.
        Yuan

      • June 2, 2011 at 7:57 pm #5694
        Anonymous

          Presumably you want to model the phosphorylated residue. I’m going to assume it’s phosphoserine, but this advice works for any of them.

          First, make sure p-ser is active in the residue type set. Go to minirosetta_database/chemical/residue_type_sets/fa_standard/patches.txt and make sure the proper phosphorylated residue type is active (NOT commented out with #). (This is default).

          Next, make sure Rosetta reads it in. Make sure your atom names in your input PDB match the atom names specified in the patch file (its path is in patches.txt). Spacing will matter here, ” P ” is different from ” P “.

          Run short trajectories as you test the PDB read in, or just run something like the score app, and look at the output to make sure Rosetta keeps the phosphoatoms in place.

          Once the PDB reader handles it, flexpepdock should as well.

        • June 2, 2011 at 9:05 pm #5695
          Anonymous

            Thanks for Smlewis’ kind reply.
            In my peptide, the p-ser is labeled “SEP” and this is not recognized by Rosetta.Where should I tell the program that “SEP” is the phosphorylated Serine?(The atom names matches well with the file you mentioned)
            I changed the definition filename of p-ser into SEP.txt,but it does not work..
            When I change the “SEP”s into “SER”, it now works fine,as it was discussed before
            http://www.rosettacommons.org/node/2310
            Thanks again.

          • June 2, 2011 at 9:32 pm #5696
            Anonymous

              In the Prepack step, it works fine.
              But in the docking step,error happens as “can not find a residue type that matches the residue SER_p:phosphorylateda….”
              And in the prepacked pdb files, the p-Ser is still “SER”, but there is one line starts with “

              SER_p:phosphorylated_***
              ERROR: switch_to_residue_type_set fails

              ERROR:: Exit from: src/core/chemical/util.cc line: 645

              ” and I think this is corresponding to my errors.
              ANyone has any suggestions?

            • June 2, 2011 at 10:51 pm #5699
              Anonymous

                Sounds like you’re having issues with there not being a p-Ser in the “centroid” residue type set. See http://www.rosettacommons.org/node/2342

                I’m not too familiar with Flexpep docking, but you might be able to avoid the centroid mode phase altogether. You may want to try omitting the “-lowres_preoptimize” flag.

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