Diego On Fri, Mar 7, 2025 at 12:50 AM DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO < [email protected]> wrote:

Dear phenixbb:

I'm working with a GTP binding protein and have had some problems running phenix_refine.

In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands

Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H "

This is because the restraints in Phenix have the v2 names while your model has v3 names.

Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped.

The file you downloaded is an information file, not restraints. I have generated restraints using eLBOW (attached). Nigel

Since I'm in the initial stages of the refinement I'm running phenix with bindividuals.

Could anybody save my day giving me some light into this issue?

Cheers,

Diego

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