Hi Rosetta community,
Hoping someone can help me with this issue I'm having! I'm trying to dock a cofactor and a ligand into an alphafold model using Rosetta match. Essentially, I know which residue is supposed to be covalently bound to the cofactor, so I've made that the first constraint block of the CST file. Then, I am trying to match the ligand with the cofactor. This is constraint block #2 and as such I have included the following lines at the end of CST block 2 (since I'm matching essentially ligand 1 to ligand 2).
ALGORITHM_INFO:: match
SECONDARY_MATCH: DOWNSTREAM
ALGORITHM_INFO::END
CST::END
When I try to dock, I get the following error:
WARNING: Override of option -match:lig_name sets a different value
ERROR: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed.
ERROR:: Exit from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line: 1210
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
match_1.sh: line 13: 30217 Segmentation fault /home/a1love/rosetta_src_2021.16.61629_bundle/main/source/bin/match.linuxgccrelease -extra_res_fa ./FAD.params -extra_res_fa ./LCA.params -match:geometric_constraint_file ./ACL_CST_2.cst -match:lig_name FAD -match:lig_name LCA -match:scaffold_active_site_residues_for_geomcsts /home/a1love/..../ACL_pos.pos -out:path:all /home/a1love/....../RosettaDock/docking -s ./enz_rlx_0001.pdb @general_match.flags > match.log
This is the CST file:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: C8M C8 C9
TEMPLATE:: ATOM_MAP: 1 residue3: FAD
TEMPLATE:: ATOM_MAP: 2 atom_type: Nhis,
TEMPLATE:: ATOM_MAP: 2 residue1: H
CONSTRAINT:: distanceAB: 1.60 0.5 80.0 1 1
CONSTRAINT:: angle_A: 125.2 10.0 10.0 360. 1
CONSTRAINT:: angle_B: 92.1 10.0 10.0 360. 1
CONSTRAINT:: torsion_A: 3.3 10.0 10.0 360. 1
CONSTRAINT:: torsion_AB: -109.7 10.0 10.0 360. 1
CONSTRAINT:: torsion_B: 94.0 10.0 10.0 360. 1
CST::END
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: C8 C17 C12
TEMPLATE:: ATOM_MAP: 1 residue3: LCA
TEMPLATE:: ATOM_MAP: 2 atom_name: N5 C5X C6
TEMPLATE:: ATOM_MAP: 2 residue3: FAD
CONSTRAINT:: distanceAB: 3.70 1.3 80.0 0 1
CONSTRAINT:: angle_A: 38.7 10.0 10.0 360. 1
CONSTRAINT:: angle_B: 98.5 10.0 10.0 360. 1
CONSTRAINT:: torsion_A: 70.8 10.0 10.0 360. 1
CONSTRAINT:: torsion_AB: -136.6 10.0 10.0 360. 1
CONSTRAINT:: torsion_B: -66.6 10.0 10.0 360. 1
ALGORITHM_INFO:: match
SECONDARY_MATCH: DOWNSTREAM
ALGORITHM_INFO::END
CST::END
This is the text of the pos file:
N_CST 2
1: 67
2: all
I've tried troubleshooting this issue and here's what I've found. If I comment out the second constraint block and remove the scond line of the pos file, I get successful matches. So the issue is with the second constraint block. I'm very new to Rosetta, so I'm a bit lost on what to do next. I'm attaching here also the ROSETTA_CRASH.log and the match.log since that could be helpful. Let me know if there's any other information I can provide that would help troubleshoot the issue. I have not tried running in debuggar mode because it's not clear to me how to actually install debuggar mode or run it :( if that's the next step I should try, if someone could please let me know how I should actually do that that would be amazing. Any help/advice/suggestions would be greatly appreciated!!!!!!!
| Attachment | Size |
|---|---|
 ROSETTA_CRASH.log | 3.42 KB |
| match.log | 17.07 KB |
To my understanding, the match algorithm is set up to place a single ligand only. That warning message ("WARNING: Override of option -match:lig_name sets a different value") is indicating that putting -match:lig_name twice on the command line isn't doing what you think it's doing (it's only taking the latter, not both.)
If you have two ligands to place by matching, I would recommend a sequential approach. First fully match the first ligand in one run, then match the second ligand in a separate matcher run (with separate constraint file). If you get multiple match positions for the first ligand, you should be able to use all such results as the templates for the second match run. (The matcher is set up to run across multiple template sets.)
Once you have both matched, you should be able to use a merged constraint file for any downstream enzyme design usage, but for the matcher proper you'll need to concentrate on one ligand at a time.
Okay that makes sense thank you for the help!! I guess I was confused reading through the matcher CST file information (https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/match-cstfile-format) and thought I could match one ligand to the other ligand from the upstream CST block. I will definitely try out the sequential approach as I already have matchs from the first CST block which ran no problem.
One more question for you - for the sequential approach you suggest, to use all the match results from the first ligand run for the second match run, can I just specify the match script "-s" parameter where I specify the pdb file, can I just put /path/to/files/*.pdb? To specify that all .pdb files in that directory should be used for matching? Or is there another shorthand way to let the matcher know to use all the previous match results that doesn't involve having a bunch of different -s lines?Thank you so much for your help!! I really appreciate it!
Okay I tried sequential docking and I am still getting the same error although the contents of the match log are slightly different.
This is the updated CST file
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: C8 C17 C12
TEMPLATE:: ATOM_MAP: 1 residue3: LCA
TEMPLATE:: ATOM_MAP: 2 atom_name: N5 C5X C6
TEMPLATE:: ATOM_MAP: 2 residue3: FAD
CONSTRAINT:: distanceAB: 3.70 1.3 80.0 0 1
CONSTRAINT:: angle_A: 38.7 10.0 10.0 360. 1
CONSTRAINT:: angle_B: 98.5 10.0 10.0 360. 1
CONSTRAINT:: torsion_A: 70.8 10.0 10.0 360. 1
CONSTRAINT:: torsion_AB: -136.6 10.0 10.0 360. 1
CONSTRAINT:: torsion_B: -66.6 10.0 10.0 360. 1
CST::END
I'm attaching the match.log here as well if that is helpful!! Any advice is appreciated!!