Error while running BINANA

Computer-Aided Drug Design at the Durrant Lab Forums BINANA Error while running BINANA

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    • #110208 Reply
      Chandan
      Guest

      Hello Prof. Durrant,

      I get the following error with the BINANA code.
      The input recepor is as follows (snippet)
      #########################
      ATOM 65 N LYS A 5 -25.636 8.362 45.227 1.00 34.78 -0.229 NA
      ATOM 66 CA LYS A 5 -25.667 9.020 46.528 1.00 36.92 0.186 C
      ATOM 67 C LYS A 5 -25.399 10.504 46.317 1.00 32.31 0.274 C
      ATOM 68 O LYS A 5 -24.261 10.908 46.053 1.00 37.11 -0.268 OA
      ATOM 69 CB LYS A 5 -24.643 8.396 47.471 1.00 39.24 0.034 C
      ATOM 70 CG LYS A 5 -25.062 8.413 48.934 1.00 39.96 0.005 C
      ATOM 71 CD LYS A 5 -24.326 7.353 49.740 1.00 43.24 0.041 C
      ATOM 72 CE LYS A 5 -24.965 5.984 49.571 1.00 48.83 0.338 C
      ATOM 73 NZ LYS A 5 -24.162 4.914 50.226 1.00 58.11 0.618 N
      ATOM 87 N MET A 6 -26.446 11.316 46.414 1.00 25.57 -0.229 NA
      ATOM 88 CA MET A 6 -26.400 12.716 46.023 1.00 36.94 0.187 C
      ATOM 89 C MET A 6 -26.467 13.607 47.255 1.00 30.91 0.274 C
      ATOM 90 O MET A 6 -27.368 13.459 48.088 1.00 28.98 -0.268 OA
      ATOM 91 CB MET A 6 -27.548 13.047 45.068 1.00 32.35 0.046 C
      ATOM 92 CG MET A 6 -27.370 14.341 44.297 1.00 41.91 0.060 C
      ATOM 93 SD MET A 6 -28.586 14.521 42.977 1.00 50.06 -0.139 SA
      ATOM 94 CE MET A 6 -28.245 13.061 41.999 1.00 42.04 0.069 C

      #########################

      WARNING: There is no atom named "N" in the protein residue LYS_5_A. Please use
      standard naming conventions for all protein residues to improve BINANA accuracy.

      WARNING: There is no atom named "C" in the protein residue LYS_5_A. Please use
      standard naming conventions for all protein residues to improve BINANA accuracy.

      WARNING: There is no atom named "CA" in the protein residue LYS_5_A. Please use
      standard naming conventions for all protein residues to improve BINANA accuracy.

      WARNING: There is no atom named "N" in the protein residue MET_6_A. Please use
      standard naming conventions for all protein residues to improve BINANA accuracy.

      WARNING: There is no atom named "C" in the protein residue MET_6_A. Please use
      standard naming conventions for all protein residues to improve BINANA accuracy.

      I donot understand what could have gone wrong with the input. The input was generated using Autodock tools.

      Thank you!

      Chandan

    • #130929 Reply
      Jacob Durrant
      Keymaster

      Hi Chandan. Is the text you provided in your question the original PDB text? I ask because that PDB text isn’t valid, though it could be a problem that arose when you pasted the PDB file into the forum text box.

      Entries in PDB files are determined by column, so it’s critical to put all the spaces in the right places. They are not simply space-delimited fields, if that makes sense.

      Hope this answer helps. Take care.

      ~Jacob

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