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Hi can anyone help?
I have tried to set up a simulated anneal run for a 60 AA protein,
The SA seems to be going fine and then reports:
%ATMCHK-ERR: unknown coordinates for atom " -16 -HIS -ND1 "
and the SA ends.
I'm out of ideas as to what I can do next. I am also a bit puzzled as
to why it is the same atom that is lost each time even though the
energy input from the temperature bath is meant to be randomly
distributed and I have used 2 different pdb files with slightly
different starting coordinates.
I would be most greatful for any suggestions.
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It is still probable that your ND1 atoms "flies away" from
your His. Have you checked the charge status of your histidine
and its immediate neighbors.
If you use an all atom force field and you succed in minimizing the
structure, this error is unlikely to occur