# Per-residue energy analysis

**URL:** <https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763>\
**Category:** HADDOCK\
**Created:** [June 16, 2022, 6:28am UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763 "2022-06-16T06:28:51Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Warren](https://avatars.discourse-cdn.com/v4/letter/w/97f17d/32.png) [@Warren](https://ask.bioexcel.eu/u/Warren)\
**Post date:** [June 16, 2022, 6:28am UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/1 "2022-06-16T06:28:51Z")

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hi，all，  
I want to analysis per-residue energy , I have read the manual [HADDOCK2.4 manual - Analysis – Bonvin Lab](https://www.bonvinlab.org/software/haddock2.4/analysis/#per-residue-energy-analysis), 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.

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 19, 2022, 2:44pm UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/2 "2022-06-19T14:44:25Z")

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

```auto
{======================= 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.

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**Author:** ![Marija](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marija/32/278_2.png) [@Marija](https://ask.bioexcel.eu/u/Marija)\
**Post date:** [May 3, 2023, 12:21pm UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/3 "2023-05-03T12:21:36Z")

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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:

> **[Advanced refinement of molecular complexes](https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/)**

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

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [May 3, 2023, 12:39pm UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/4 "2023-05-03T12:39:31Z")

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> • 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:

```auto
  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:

```auto
  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:

```auto
  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:

```auto
      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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<div class="post-metadata">

**Author:** ![Marija](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marija/32/278_2.png) [@Marija](https://ask.bioexcel.eu/u/Marija)\
**Post date:** [May 3, 2023, 1:33pm UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/5 "2023-05-03T13:33:31Z")

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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?

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [May 3, 2023, 1:54pm UTC](https://ask.bioexcel.eu/t/per-residue-energy-analysis/3763/6 "2023-05-03T13:54:02Z")

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