[phenixbb] Error with Phenix refine after adding ligand

Mian-Chee Gor m.gor at griffith.edu.au
Mon Jan 22 21:20:54 PST 2018

Hello all,

I run into this problem when I tried to refine my protein structure after
adding ligand.

The ligand that I am adding is a malonate, and the 3-letter chemical code
is MLI. I add the ligand using Coot and it fit perfectly into the electron
density map.

I then tried to run phenix.refine by giving the protein structure pdb file,
the original mtz file and the protein sequence fasta file. However, there
was an error message saying missing restraints for the ligand. So I
generate the CIF file for the ligand using the Ready Set icon in the
toolbar. The ligand CIF file and a updated protein structure pdb file was
generated and automatically added to the refinement windows. However, when
I run the refinement, I saw this error message: Number of nonbonded
interaction distances <0.001:2. Please inspect the output above (or in the
log window) and correct the input model file.

When I inspect the log window, the error is due to the oxygen atoms in the
ligand being too close to each other. Why is there an error if the ligand
was generated automatically in Phenix? Has anyone encounter this problem
before? How do you solve that?

Many thanks in advance!

Dr Mian-Chee Gor
Research Fellow
Griffith Institute for Drug Discovery (GRIDD)
Don Young Road, Nathan, QLD 4111
Mobile: +61 4 2084 7785
Email: m.gor at griffith.edu.au
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