<div dir="ltr">Hi Danilo,<div><br></div><div>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.</div><div>The number 14 refers to the number of atoms, not the energy type symbol.</div><div><br></div><div>Once we know which atoms cause problems, we can help more.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Jan 11, 2019 at 5:13 AM Danilo Belviso <<a href="mailto:danilo.belviso@ic.cnr.it" target="_blank">danilo.belviso@ic.cnr.it</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear all,<br>
<br>
I am refining the structure of a cyclic peptide with having residues <br>
that are not in the ligand list of phenix.<br>
<br>
I would to perform unrestrained refinement by considering the very good <br>
resolution of the data. However, also in this case, phenix requires the <br>
restrain file of the ligand.<br>
<br>
I got cif file in two different way:<br>
<br>
1) PRODRG server<br>
2) by running phenix.elbow<br>
<br>
both produce the restrain file with no error message. However, by using <br>
such file in the refining, I get this error:<br>
<br>
Sorry: Fatal problems interpreting model file:<br>
Number of atoms with unknown nonbonded energy type symbols: 14<br>
<br>
In the cif file, there are not atoms having 14 as energy type symbols.<br>
<br>
Could you suggest to what this message is referred to?<br>
How can I modify the cif to overcome the problem?<br>
<br>
Thanks in advance,<br>
<br>
Danilo<br>
<br>
-- <br>
Dr. Belviso Benny Danilo, PhD<br>
Istituto di Cristallografia (IC)<br>
Consiglio Nazionale delle Ricerche (CNR)<br>
via Amendola 122/o, 70126 Bari - Italy<br>
Tel ++39 080 5929273<br>
Fax ++39 080 5929170<br>
mail: <a href="mailto:danilo.belviso@ic.cnr.it" target="_blank">danilo.belviso@ic.cnr.it</a><br>
web: <a href="http://users.ba.cnr.it/ic/crisdb00" rel="noreferrer" target="_blank">users.ba.cnr.it/ic/crisdb00</a><br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br>
</blockquote></div>