[phenixbb] pdb file error

[maher alayyoubi]

Hi Everyone,
I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part.
Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located"
Does anyone know how to fix this problem?
I tried converting the file into mmcif and feeding it to phenix but the same error comes back again.

Thank you very much,
Maher
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