Hi,
From your email, I *think* what you're looking for is a way to analyze what
ions are doing during simulations.
You can use commands in Cpptraj to analyze ions' behavior.
Typically, I use things like 'closest' 'hbond' and 'grid' in various ways -
take a look at the Amber Manual entries for these commands.
The analysis and scripts I used are included in Supporting Information of
these papers:
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b05190
https://www.sciencedirect.com/science/article/pii/S000634951730629X
Good luck, hope this helps.
-Christina
On Wed, Dec 9, 2020 at 4:26 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Wed Dec 09 2020 - 06:00:04 PST
