Bond constraints and KeyError

[darthmodel]

Hi,

Can someone help me understand how to set up bond constraint? I can't seem to get boltz to correctly parse the yaml file. Here is the constrain section.

constraints:
  - bond:
      atom1: [A, 77, NZ]
      atom2: [C, 1, O72]
  - bond:
      atom1: [A, 8, NZ]
      atom2: [C, 1, O12]

It always ends up with a KeyError on atom1 of the first bond. Is it because constraints are only available through the github repo. I installed mine via pip install boltz.

Thanks,
G

[gcorso]

Hi @darthmodel could you share a full input file for us to reproduce the error?

[darthmodel]

Hi @gcorso thanks for getting back and also for making the model available. Here is the input file.

version: 1
sequences:
  - protein:
      id: [A]
      sequence: "SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG"
      msa: /path/to/chainA.a3m
  - protein:
      id: [B]
      sequence: "AQVQLQESGGGLVQAGGSLRLSCAASERTFSTYAMGWFRQAPGREREFLAQINWSGTTTYYAESVKDRTTISRDNAKNTVYLEMNNLNADDTGIYFCAAHPQRGWGSTLGWTYWGQGTQVTVS"
      msa: /path/to/chainB.a3m
  - ligand:
      id: [C]
      ccd: PML
constraints:
  - bond:
      atom1: [A, 77, NZ]
      atom2: [C, 1, O72]
  - bond:
      atom1: [A, 8, NZ]
      atom2: [C, 1, O12]

If I recall correctly, I also tried no MSA and got the same error. Once again, your time is greatly appreciated.

Best,
G