[phenixbb] atoms with unknown nonbonded energy type

Dorothee Liebschner dcliebschner at lbl.gov
Fri Jan 11 14:04:29 PST 2019

Hi Danilo,

After the sentence "Number of atoms with unknown nonbonded energy type
symbols: 14", there should be a few examples of atoms for which no energy
type was found.
The number 14 refers to the number of atoms, not the energy type symbol.

Once we know which atoms cause problems, we can help more.

Best wishes,


On Fri, Jan 11, 2019 at 5:13 AM Danilo Belviso <danilo.belviso at ic.cnr.it>

> Dear all,
> I am refining the structure of a cyclic peptide with having residues
> that are not in the ligand list of phenix.
> I would to perform unrestrained refinement by considering the very good
> resolution of the data. However, also in this case, phenix requires the
> restrain file of the ligand.
> I got cif file in two different way:
> 1) PRODRG server
> 2) by running phenix.elbow
> both produce the restrain file with no error message. However, by using
> such file in the refining, I get this error:
> Sorry: Fatal problems interpreting model file:
>    Number of atoms with unknown nonbonded energy type symbols: 14
> In the cif file, there are not atoms having 14 as energy type symbols.
> Could you suggest to what this message is referred to?
> How can I modify the cif to overcome the problem?
> Thanks in advance,
> Danilo
> --
> Dr. Belviso Benny Danilo, PhD
> Istituto di Cristallografia (IC)
> Consiglio Nazionale delle Ricerche (CNR)
> via Amendola 122/o, 70126 Bari - Italy
> Tel ++39 080 5929273
> Fax ++39 080 5929170
> mail: danilo.belviso at ic.cnr.it
> web: users.ba.cnr.it/ic/crisdb00
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