It seems to that pdb4amber identifies phosphorylated amino acids (e.g.,
TPO) as non-standard residues and switches them to HETATM entries flanked
by TER chars. The output notifies the user of the first part, but not the
second. Putting the output through tleap leads to spurious termini around
the phosphorylated residues. I would consider this unexpected, if not a bug.
A reasonable example from the PDB is 4ztn, although this also has missing
loops.
Cheers,
Brian
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Received on Thu Feb 10 2022 - 12:00:02 PST
