Haddock3 provides different output scores

HADDOCK
1

Hi,

I conducted an ab-initio docking analysis on the E2A-HPR complex using haddock3. I selected this protein complex based on its inclusion as an example in your HADDOCK2.4 documentation. This choice facilitated a comparison of the scoring metrics, allowing me to assess whether my ab-initio protocol is optimal and capable of reproducing similar results to those presented in your documentation.

Upon comparing my results with yours, I observed discrepancies in the output. Specifically, my output lacks information on the z-score and Restraints Violation Energy. I have attached a screenshot of my output for your reference.

Additionally, I have a question regarding the “restraints energy” score in my results, which is recorded as 0. I couldn’t find information in the HADDOCK documentation explaining the meaning of the “restraints energy” score and what a value of 0 indicates. Could you please provide clarification on this matter?

Thank you for your assistance.

haddock_result_analysis
haddock_result_analysis1284Ă—678 139 KB

2

The z-score is simply reporting the number of standard deviations from the mean.

We don’t find it very useful and decided to remove it. You can of course easily calculate it.

As for the restraint energy, depending on what you ab-initio protocol is, it is not surprising it might be zero.

But without viewing your protocol we can’t say for sure.

3

@amjjbonvin
Thank you, Professor, for your prompt response. I initially employed a center of mass for restraining energy; however, I would like to provide an example of my ab-initio protocol. I hope this example will help you further clarify the concept of restraint energy scores for me.

    run_dir = "complexe_ref_docking"
    #mode = 'mpi'
    ncores = 40

    mode = "local"
    # molecules to be docked
    molecules =  [
        "e2a_1F3G.pdb",
        "hpr-ensemble.pdb"
        ]
    # CNS executable path - optional
    #cns_exec = "/software/haddock3/bin/cns"

    [topoaa]
    autohis = true

    [rigidbody]
    tolerance = 20
    sampling = 10000
    cmrest = true
    cmtight = true
    kcm = 1.0
    ncs_on = false
    ntrials = 1
    npart = 1.1428
    
    [caprieval]

    [seletop]
    select = 400

    [flexref]
    cmrest = true
    cmtight = true
    kcm = 1.0
    ncs_on = false
    sampling_factor = 1
    #max_nmodels = 400
    
    #[caprieval]

    [seletop]
    select = 400

    [emref]
    #max_nmodels = 400
    nemsteps = 500
    
    #[caprieval]

    [seletop]
    select = 400

    [mdref]
    #max_nmodels = 400
    solvent = 'water'
    nemsteps = 500
    timestep = 0.002
    waterheatsteps = 500
    watersteps = 1000
    watercoolsteps = 1000
    
    

    [seletop]
    select = 400

    #[caprieval]
    [ilrmsdmatrix]
    
    [clustrmsd]
    criterion = 'distance'
    #linkage = 'average'
    #threshold = 4 

    [seletopclusts]

    #tolerance = 20
    ## select the best 4 clusters
    top_cluster = 5
    ## select all the clusters

    ## select the best 4 models of each cluster
    top_models = 20
    ##select all the models
    #top_models = NaN
    
    [caprieval]

    [emscoring]
    w_bsa = 0.0
    w_cdih = 0.0
    w_desolv = 1.0
    w_elec = 0.2
    w_vdw = 1.0
    elecflag = true
    dielec = 'cdie'
    epsilon = 1.0
    dihedflag = true
    nemsteps = 10000
    
    [caprieval]
4

Since you have no restraints in the emref and mdref stages the restraint energy is simply 0

5

@amjjbonvin
According to my understanding of restraint energy in the fields of molecular docking and molecular dynamics, restraint energy is generally associated with the energy resulting from constraints applied during simulation to replicate experimental information or known structures. This helps guide simulations towards more realistic conformations or explore specific interactions. Therefore, do you think it is necessary to add them to my protocol? Considering that I have chosen to perform ab-initio docking as I have no experimental information on the proteins I wish to study.
What I mean is, can we do without it? If we don’t apply restraint energy to the emref and mdref phases, will my results and analyses be biased?

6

There is no problem not include any restraints. Especially if you want to follow an ab initio docking protocol.

1 Like