wrote:
Hello everybody, i have a question about the output-file evaluate_model.log. I looked in the basic_example from the Modellers Homepage and also in my own output files. In the most of the cases there is the following message: report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1 2 1.480 serious non-bonded atom clash: 2 3 1.539 serious non-bonded atom clash: 2 7 1.493 serious non-bonded atom clash: 3 4 1.528 serious non-bonded atom clash: 4 5 1.817 serious non-bonded atom clash: 5 6 1.816 .... Can everybody explain what does it exactly mean? Is for example the number 1 the first atom in the template and 2 the second in the model or what does it mean? And what can i do that this message never comes?
The atom numbers refer to the model, not the template (the template is never changed during optimization, and is not considered at all during model evaluation). Thus, it's saying that the first and second atoms in your model are only 1.480A apart, and so on. (To find out which atoms these are, look in your PDB file, since the order there should be the same.)
Modeller warns about all pairs of atoms that are very close together when evaluating non-bonded interactions (such as Lennard Jones, Coulomb, or DOPE energies) since generally non-bonded atoms would not be in such close contact (if they were, it would suggest a covalent bond or other bonded interaction). However, I suspect you are doing DOPE evaluation here, in which case the warnings can be disregarded; DOPE considers _all_ pair interactions, even bonded atoms, and so many nearby atom pairs will be considered.
Ben Webb, Modeller Caretaker
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