[phenixbb] atoms with unknown nonbonded energy type

Danilo Belviso danilo.belviso at ic.cnr.it
Fri Jan 11 05:10:19 PST 2019

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,


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

More information about the phenixbb mailing list