# Analysis energies **URL:** \ **Category:** HADDOCK\ **Created:** [February 16, 2024, 10:20am UTC](https://ask.bioexcel.eu/t/analysis-energies/4841 "2024-02-16T10:20:52Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [February 16, 2024, 10:20am UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/1 "2024-02-16T10:20:52Z")
Hi how come in the file ene-residue.disp the intermolecular energies sometimes equal 0. For example #Residue ALA 20 A - intermolecular energies #file Etot Evdw Eelec # PREVIT:HADDOCK\_207w.pdb -4.270315E-05 -4.270315E-05 0 # PREVIT:HADDOCK\_233w.pdb 0 0 0 # PREVIT:HADDOCK\_132w.pdb 0 0 0 # PREVIT:HADDOCK\_321w.pdb 0 0 0 # PREVIT:HADDOCK\_164w.pdb 0 0 0 # PREVIT:HADDOCK\_357w.pdb -0.542999 -0.153957 -0.389042 # PREVIT:HADDOCK\_142w.pdb 0 0 0 # PREVIT:HADDOCK\_91w.pdb -8.64886E-02 -6.167295E-02 -2.481565E-02 And in ene-residue.disp all in intermolecular energies sections equal 0 #Proteins flexible interface energies #file Etot Evdw Eelec # PREVIT:HADDOCK\_207w.pdb 0 0 0 # PREVIT:HADDOCK\_233w.pdb 0 0 0 # PREVIT:HADDOCK\_132w.pdb 0 0 0 # PREVIT:HADDOCK\_321w.pdb 0 0 0 # PREVIT:HADDOCK\_164w.pdb 0 0 0 # PREVIT:HADDOCK\_357w.pdb 0 0 0 # PREVIT:HADDOCK\_142w.pdb 0 0 0 # PREVIT:HADDOCK\_91w.pdb 0 0 0 # PREVIT:HADDOCK\_342w.pdb 0 0 0 # PREVIT:HADDOCK\_147w.pdb 0 0 0 # PREVIT:HADDOCK\_343w.pdb 0 0 0 # PREVIT:HADDOCK\_136w.pdb 0 0 0 # PREVIT:HADDOCK\_331w.pdb 0 0 0 # PREVIT:HADDOCK\_39w.pdb 0 0 0 # PREVIT:HADDOCK\_151w.pdb 0 0 0 # PREVIT:HADDOCK\_72w.pdb 0 0 0 # PREVIT:HADDOCK\_382w.pdb 0 0 0 # PREVIT:HADDOCK\_298w.pdb 0 0 0 # PREVIT:HADDOCK\_325w.pdb 0 0 0 # PREVIT:HADDOCK\_43w.pdb 0 0 0 The docking has fully flexible in peptides and protein. Best, Miriam ---
**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:** [February 16, 2024, 7:05pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/2 "2024-02-16T19:05:38Z")
The script first finds all residues involved in contacts by analysing all models and then performs the energetic analysis of all of those. As a result, unless all models would have overlapping interfaces, you will have models with 0 energies for a given residue because it is simply not in the interface of that model. ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [February 17, 2024, 4:51pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/3 "2024-02-17T16:51:04Z")
Thank you, I understand why some of the energies for a certain residue will equal 0, but I still don’t understand why in energies.disp the section for “#Proteins flexible interface energies” will all be zero, when some of the amino acids have interaction energy (which are also seen in low values in ene-residue.disp (-143.8) ---
**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:** [February 17, 2024, 7:07pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/4 "2024-02-17T19:07:09Z")
Are you speaking about the `energies.disp` file, a different one? This one lists energies per model and not per amino acids. Those energies are indeed zero when the flexibility is set to automatic mode. But all the energies you want to look at are in the header of the PDB files and can be extracted with the `ana_structures.csh` script. ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [February 17, 2024, 7:35pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/5 "2024-02-17T19:35:15Z")
yes, I am speaking about energies.disp file. I made some of the amino acids fully flexible, is that not “flexibility is set to automatic mode”? So why are all flexible interface energies equal to 0? #Proteins flexible interface energies #file Etot Evdw Eelec # PREVIT:HADDOCK\_207w.pdb 0 0 0 # PREVIT:HADDOCK\_233w.pdb 0 0 0 # PREVIT:HADDOCK\_132w.pdb 0 0 0 # PREVIT:HADDOCK\_286w.pdb 0 0 0 Another question: What does CLASS DIST mean in print\_noe\*out file? how come some of the restraints are listed more than once? are they separated by structures? How can I see which structures each violation belongs to? Thank you ---
**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:** [February 17, 2024, 8:03pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/6 "2024-02-17T20:03:10Z")
Simply extract the energies from the PDB headers The energy.inp script is simply outdated and only considers the semi-flexible segments for that section. We should remove that part ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [February 17, 2024, 8:14pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/7 "2024-02-17T20:14:22Z")
Thank you And regarding the last question, What does CLASS DIST mean in print\_noe\*out file? how come some of the restraints are listed more than once? are they separated by structures? How can I see which structures each violation belongs to? ---
**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:** [February 18, 2024, 12:13pm UTC](https://ask.bioexcel.eu/t/analysis-energies/4841/8 "2024-02-18T12:13:45Z")
> What does CLASS DIST mean in print\_noe\*out file? All distance restraints (both ambiguous and unambiguous). I would only really look at the ambig unambiguous ones. There is indeed some duplication. > how come some of the restraints are listed more than once? are they separated by structures? How can I see which structures each violation belongs to? The info is in principle in the out file, but not simply to extract. I would recommend to perform a per cluster analysis, e.g. selecting the top4 models of each cluster. If you repeat the analysis you will get the restraint stats for a specific cluster.