[phenixbb] unrestrained refinement

[Nigel Moriarty]

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

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Tue, Dec 18, 2018 at 3:01 PM Kaiser, Jens T. <kaiser at caltech.edu> 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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