Thank you for your answer. Masses for those oxygens are correct. I
attach tleap script by which prmtop was prepared.
Juraj
On 02. 02. 24 22:24, David A Case via AMBER wrote:
> 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 Mon Feb 05 2024 - 01:00:02 PST
