Hello HADDOCK team,
I am troubleshooting an αVβ3–GRGDSP peptide complex containing 8 Mn2+ ions and 1,466 receptor residues, submitted through the HADDOCK 2.4 webserver.
The archived run contains completed it0, it1 and final-refinement models, although the portal reports “Failed”. Metal geometry is acceptable in it1, but the final refinement produces very short Mn–O contacts, approximately 1.4–1.5 Å.
The downloaded run.cns retains nseg_1=0 and nfle_1=0 for the receptor. However, receptor heavy atoms still move during the final stage, with a maximum direct displacement of approximately 2.20 Å relative to it1. The run uses solvshell=false, so this is not explicit-water MD.
I have prepared a diagnostic modification to re_h2o.inp that explicitly reapplies receptor-heavy-atom fixation, including the Mn ions, before each minimization. This is a hypothesis to test, not a confirmed explanation of the failure.
Could you please clarify:
- Does the webserver support a custom CNS protocol (.inp), or equivalent supported parameters for this diagnostic?
- Can final refinement be restarted from the existing it1 complex while preserving its paired PSF, parameters and 39 distance restraints, without rerunning it0/it1?
- What is the recommended way to preserve receptor fixation and metal-site geometry during final refinement?
The Refinement interface currently exposes only clustering and analysis settings after PDB upload, and “Param file + input” is marked temporarily disabled.
I can provide the relevant run.cns settings, protocol excerpt and selected coordinates if helpful.
Thank you.
Hi there
Would you have a jobID for this run so that we can investigate?
Note that you can always use models from it1 and skip the final minimisation.
The archived run contains completed it0, it1 and final-refinement models, although the portal reports “Failed”. Metal geometry is acceptable in it1, but the final refinement produces very short Mn–O contacts, approximately 1.4–1.5 Å.
The downloaded run.cns retains nseg_1=0 and nfle_1=0 for the receptor. However, receptor heavy atoms still move during the final stage, with a maximum direct displacement of approximately 2.20 Å relative to it1. The run uses solvshell=false, so this is not explicit-water MD.
I have prepared a diagnostic modification to re_h2o.inp that explicitly reapplies receptor-heavy-atom fixation, including the Mn ions, before each minimization. This is a hypothesis to test, not a confirmed explanation of the failure.
Could you please clarify:
- Does the webserver support a custom CNS protocol (.inp), or equivalent supported parameters for this diagnostic?
No - but at guru level you can control quite a lot of parameters.
Note that another option would be to provide unambiguous distance restraints to restrain the MN distance to its coordinating atoms.
- Can final refinement be restarted from the existing it1 complex while preserving its paired PSF, parameters and 39 distance restraints, without rerunning it0/it1?
Only when running a local version of HADDOCK
- What is the recommended way to preserve receptor fixation and metal-site geometry during final refinement?
The Refinement interface currently exposes only clustering and analysis settings after PDB upload, and “Param file + input” is marked temporarily disabled.
You can choose various protocols, like EM only, or water refinement.