You are here

Home » Forums » Rosetta 3 » Rosetta 3 - General

Error when using published constraints file

3 posts / 0 new
Log in or register to post comments
Last post
Error when using published constraints file
#1
Top

Hello,

I am attempting to follow a recent publication released by the Baker group. I am using this cst file to constrain an iron atom to a histidine:

https://github.com/ikalvet/heme_binder_design/blob/main/theozyme/HMM/HMM_His.cst

I have renamed the HMM residue to match with my ligand name.

However I am getting errors about the format of the cstfile. When I run design the program errors after 6 seconds with the following errors:

ERROR: Undefined error when reading cstfile. Something is wrong with the format (no CST::END tag maybe? ).

There is definitely a CST::END tag however, so I am not sure why I am getting this error. 

Thanks,

Elliot

This is the output arround the error:

basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /share/apps/rosetta/bin/../database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/share/apps/rosetta/bin/../database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.2 seconds to load from binary
protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: Error, when reading algorithm info block with tag match, no ALGORITHM_INFO::END line was found.
Error: [ ERROR ] Must call shutdown() when finished using job distributor!
protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from His.cst ...
protocols.toolbox.match_enzdes_util.EnzConstraintIO: [ WARNING ] Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicitly call Tracer::flush() or end your IO with std::endl to disable this warning.
 

 

Category: 
Design
Post Situation: 
Unsolved
Thu, 2023-08-17 11:22
Delfosse57
Top

I have a few suggestions. They may or may not solve your problem, but these files are sensitive.

  1. I think there should be a comma at the end of line 17 (after Nhis). I've never figured out why this comma needs to be there, though. 
  2. Most of the file uses a tab size of two spaces, but the MAX_DUNBRACK_ENERGY line has a tab size of three spaces. Really, I doubt this is it because there's an integration test with a tab size of one or two.
  3. In tests/integration/tests/cstfile_to_theozyme_pdb/inputs/CTP_RKRE_1acid2acid.cst, all of the Algorithm info tags are paired with another bit of information, whereas this one is a singleton. Do you need to provide something else?

 

I submitted an Issue on the GitHub page you linked, with a link to here. Hopefully the author will fix the problem on GitHub or provide some guidance here.

Best of luck in pursuing this!

Thu, 2023-08-17 15:15
nannemdp
Top

Thank you for bringing this to our attention! I tried to reproduce the error you're seeing with the files on my GitHub repo and I'm not able to.

Are you also seeing this error when using exactly the same files, with no modifications?

The only way I was able to see the error you're seeing was when I added a space to before "END" in this line:

"ALGORITHM_INFO::END"   ---->  "ALGORITHM_INFO:: END"

If this isn't the issue then would you perhaps mind sharing the contents of the CST file you're trying to use?

 

Mon, 2023-08-21 05:52
ikalvet