On Fri, Feb 02, 2024, Juraj Dobias via AMBER wrote:
>
>I noticed that problematic oxygens from ATP have ATOMIC_NUMBER -1 in
>.parm7 file. I don't know why, but after manually correcting them to
>8, QM/MM seems to work properly. Does anybody know how could this
>happen? I am also wondering if it could possibly influence classical
>MD?
I'm not sure how the prmtop was built. But for classical MD, the atomic
number is not used. You might want to double check (using parmed) that the
mass of those oxygens in correct.
...good luck...dac
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Received on Fri Feb 02 2024 - 13:30:02 PST
