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, Dorothee On Fri, Jan 11, 2019 at 5:13 AM Danilo Belviso wrote:

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: [email protected] web: users.ba.cnr.it/ic/crisdb00 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]