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
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.
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)
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.
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?
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
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?