Cterm_amidation

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    • November 3, 2021 at 3:52 pm #3862
      Anonymous

         

        Hi there,

        I am trying to run Flexpepdock for several peptides which have Cterm_amide group. I checked the ATOM TYPES for NH2 which are also correct but while reading pdb it always gives warning:

        core.chemical.Patch: [ WARNING ] Patch MethylatedCtermProteinFull implies it can apply to residue type TYR:Cterm_amidation, but actually applying it fails.

        core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.

        core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type TYR:Cterm_amidation, but actually applying it fails.

        core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.

        Although, the output pdb still contains Cterm_amide group but the residue is changed to NON_CANONICAL residue and ATOM name to HETATM as below:

        HETATM  195  NT  TYR B 306       9.915  21.766 -48.540  1.00  0.00            N  

        HETATM  206 1HN  TYR B 306       9.068  21.701 -49.067  1.00  0.00          H  

        HETATM  207 2HN  TYR B 306      10.780  21.900 -49.024  1.00  0.00         H

         I want to know what this warning is about and if I should ignore it??

        Beside N-terminal cap, my peptide sequence have at different amino-acid positions additional functional groups added, such as methylation, acetylation. Do I need to generate additional paramter files for those residues like mentioned in non-canonical residue papers?

        Looking forward for your expert opinion

        Mustafa

         

         

         

         

         

         

      • November 6, 2021 at 10:26 pm #16057
        Anonymous

          Hi,

          If the modification is present in the output, then the run itself should be fine.

          As for the other PTMs: most of the usual PTMs have a patch file already(I personally used phosphorylation and lysine acetylation without a problem). You can look up if any of them is missing, and create one based on their parent residue.

          Julia

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