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

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BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
#1

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
}

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Wed, 2020-04-29 01:17
daniloboskovic

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

Wed, 2020-04-29 05:41
rmoretti

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

Wed, 2020-04-29 05:51
daniloboskovic