BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?

[Anonymous]

I triple checked my protein PDB file, and i used the script to get a blueprint file. It has no chain definitions and is perfectly in order. Error happens when a succesful closure is made. If the closure is not successful, it continues. Also, if i set G or POLAR instead of ALLA, it works.

My blueprint file goes:

232 M H PIKAA M

233 F H PIKAA A

0 x L PIKAA ALLA

0 x L PIKAA ALLA

0 x L PIKAA ALLA

0 x L PIKAA ALLA

0 x L PIKAA ALLA

0 x H PIKAA A

0 x H PIKAA E

0 x H PIKAA A

0 x H PIKAA A

0 x H PIKAA A

0 X H PIKAA K

0 x H PIKAA E

0 x H PiKAA A

0 x H PIKAA A

0 x H PIKAA A

0 x H PIKAA K

0 x H PIKAA E

0 x H PIKAA A

0 x H PIKAA R

0 x H PIKAA A

0 X H PIKAA K

0 x H PIKAA E

0 x H PIKAA E

0 x H PIKAA A

0 x L PIKAA N

0 x L PIKAA P

0 x L PIKAA P

0 x L PIKAA P

234 T L PIKAA T

235 R L PIKAA R

ERROR:

File: src/core/pack/task/ResfileReader.cc:709

[ ERROR ] UtilityExitException

ERROR: Error in core::pack::task::PIKAA::add_base_name_to_keep(): The base name “LEU” was added more than once.

 

{

  “branch”: “release”,

  “date”: “2019-08-30T10:52:08.483471”,

  “git_describe”: {

    “commit”: “767c1ea”,

    “describe”: “v2019.35-dev60890-0-g767c1ea”,

    “dev_revision”: 60890,

    “post_revision”: 0,

    “week”: 35,

    “year”: 2019

  },

  “package”: “rosetta.source.release-231”,

  “revision”: 231,

  “source”: {

    “binder”: “f3f6919f73dca5b6b1d90bb0c01f8a4b24c0e2fc”,

    “demos”: “3179ab5e98f51741d988dbfcfa1169c924d43f4e”,

    “documentation”: “f127d1cd9bf76e6eb4a0ce15cc1e6c4f6aa4f53c”,

    “main”: “767c1ea25c572fbc078db45ad65dddb507240ad3”,

    “pybind11”: “35045eeef8969b7b446c64b192502ac1cbf7c451”,

    “pyrosetta_scripts”: “858903b03ea6163483f4c46802daa88c6ec4af2d”,

    “rosetta_scripts_scripts”: “55e130ac39382535ffb88ee39d0ed30163a74245”,

    “tools”: “cc80152e5bf239d826eb5c238b276fa2ad90a49e”

  },

  “url”: “https://www.rosettacommons.org”,

  “version”: “2019.35+release.767c1ea”,

  “week”: 35,

  “year”: 2019

}

[Anonymous]

Your issue is with ‘PIKAA ALLA’ . I presume you intent is say to use all amino acids. What you’re actually saying is “pick specific amino acids, the ones with the one letter codes A, L, L and A”. That’s why it’s complaining about adding LEU more than once — you have L twice there.

If you want to use all amino acids at that position, then you should drop the PIKAA, and use ALLAA instead:

         0 x L ALLAA

If you just want leucine and alanine at those positions, you keep the PIKAA, but only have them once

        0 x L PIKAA AL

[Anonymous]

Oh, i completely missed that i put ALLA and not ALLAA. Sorry. I had no idea about clustering letter codes though, thanks!

[Author]

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