I’m not sure with the problem or question is though residues should generally not be renumbered during simulation.
It is possible that different software might use 0 based or 1 based numbering which might cause problems?
Using “ambmask” or “parmed” you should be able to find the number of any atom/residue and if other software identifies something else, then just try increasing/decreasing by 1.
Best regards
// Gustaf
> On 9 Dec 2020, at 21:12, DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
>
> Dear Amber Users,
>
> Ions numbering also changes like water numbering changes during simulation.
> If yes,
> then who I will get / analyse the ions interactions.
>
> --
> ----
> Dheeraj
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Received on Wed Dec 09 2020 - 01:30:03 PST
