Hi Ming,

can you send me the PDB file or its portion that still results in problem?

Pavel

On 2/27/12 1:47 PM, Ming wrote:

Hi all,

I was trying to refine a protein with phenix.refine. I want to refine AMSE and BMET with occupancies 0.5 and 0.5.
What I did is modifying the pdb file by copy the coordinates of MET to MSE, and change the names to be AMSE and BMET, modifying the occupancy to be 0.5 and 0.5 for each one. Everything else like the atom names have been taken care of too. I used the readyset to make sure the pdb file is good. But phenix.refine keeps giving me error saying "numbers of atoms with unknown nonbonded energy type symbols ". Anyone here can help me with this please?
Thanks in advance,
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