Per-residue energy analysis

HADDOCK
1

hi，all，
I want to analysis per-residue energy , I have read the manual HADDOCK2.4 manual - Analysis – Bonvin Lab, but I have check the output files , the ene-residue.disp file inexitence.

If I want to analysis the per-residue energy, in which file do I need to difine this program . or difined in this file : read_struc.cns or run.cns ?

What line should I difined and files should be prepare.

Thank you , all.

2

You have to turn on the full analysis option - the default is only clustering.

{======================= analysis and clustering ==========================}
{* Full or limited analysis of results? *}
{+ choice: "full" "cluster" "none" +}
{===>} runana=“full";

If running locally, empty the analysis directory, change the value of the runana parameter and restart haddock.

3

Hi all,

I have a question about the per-residue energy analysis with HADDOCK 2.4.
I am performing advanced refinement using the following protocol:

  1. As far as I understand with the default parametrs only inter-chain interaction energetic scores are calculated for each residue listed in ene-residue.disp. How can I account for both, inter- and intra-chain energetics?

  2. only residues 5 Angström around the interface are included into the per-residue report in ene-residue.disp, how can I increase this threshold?

Thank you very much in advance

4

• As far as I understand with the default parametrs only inter-chain interaction energetic scores are calculated for each residue listed in ene-residue.disp. How can I account for both, inter- and intra-chain energetics?

You will have to modify the ene-residue.inp CNS script to also give you the intramolecular energies…

Line 101:

  igroup interaction (segid $iseg and resid $ires) (not segid $iseg and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO)) end

defines which interactions are considered.

If you want to have only the intromolecular energies you could modify to:

  igroup interaction (segid $iseg and resid $ires) (segid $iseg and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO)) end

(i.e. removing the not at the start of the second selection.

If you want to calculate all interactions for a given residue (i.e. both intra and inter), change line 101 to:

  igroup interaction (segid $iseg and resid $ires) (not ((resn WAT or resn HOH or resn TIP*) or resn DMSO)) end

This will only exclude any solvent present.

• only residues 5 Angström around the interface are included into the per-residue report in ene-residue.disp, how can I increase this threshold?

At line 75 of ene-residue.inp you will see:

      do (store2 = 1) (byres (segid $Toppar.prot_segid_$nchain1 and not hydrogen and
                              (not segid $Toppar.prot_segid_$nchain1 and not hydrogen) around 5.0))

Change the cutoff value after around

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5

Thank you so much for your fast and detailed reply
Can I submit the adjusted files to the web-server or I can make these adjustments only if I run HADDOCK2.4 locally on my own machine?

6

Only when running locally I am afraid.
But we could think of implementing this in the server in the future.

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