terminus capping

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    • October 7, 2009 at 6:16 pm #379
      Anonymous

        Does anyone know if it is possible to incorporate acetylation (Ac-) at the N-terminus and amidation (-NH2) at the C-terminus when doing a docking run? In my starting PDB file, these atoms are listed as HETATM and when I run dock, the output files no longer have the HETATM atoms. I have a case where the presence of these termini caps make a difference in experimental binding and would like to take a look at it using RosettaDock.

      • August 7, 2010 at 5:30 am #4556
        Anonymous

          > Does anyone know if it is possible to incorporate acetylation (Ac-) at the N-terminus and amidation (-NH2) at the C-terminus when doing a docking run? In my starting PDB file, these atoms are listed as HETATM and when I run dock, the output files no longer have the HETATM atoms. I have a case where the presence of these termini caps make a difference in experimental binding and would like to take a look at it using RosettaDock.

          Hi,
          I had the same question. Rosetta would give error saying unrecognized residue. I guess, there is no direct/simpler way to include these (based on my email conversation with the developers). Please let me know if you are able to make progress along these lines.

          Regards,
          Mohan

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