Trouble with GTP/GDP refinement.

7 Mar 2025

      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  "

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

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

DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO

Nigel Moriarty

DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO

Son Kenneth

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