Jena

UNK is, surprisingly, not a complete unknown. It is a general amino acid used for unknown amino acids. Your model contains a C81 atom which is not in the UNK restraints.

However, regardless of the existence of UNK or not, you need to provide the refinement with a restraints file whether automatically or user supplied. It is needed for the atom types and non-bonded interactions so it should contain an atom loop and a bond loop.

Cheers

Nigel

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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov

On Tue, Dec 18, 2018 at 3:01 PM Kaiser, Jens T. <[email protected]> wrote:

Hi!

I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms.

The pdb file I supply has the following format (just one line)

HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C

I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0

I also started from a default .eff file and set all references to restraints to either True of False (depending what they said).

I also tried the line from the phenix.refine documentation:

phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True

I'm using phenix v 1.14-3260 from an sbgrid environment.

Any pointers welcome.

Cheers,

Jens

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