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)

 

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