How did you get the topology and parameters for your ligand? How were the
partial charges calculated? Are there, in the protein pocket, residues that
may have different protonations like HIS?
You shouldn't have NA+ inside the enzyme pocket. Try addIonsRand instead
of addIons in tleap.
On Thu, 10 Feb 2022 at 13:52, Renato Araujo <renatoacufpa.gmail.com> wrote:
> Dear amber users
>
> I'm facing a problem in a protein-binding simulation
>
> I'm trying to simulate 100ns of molecular dynamics.
>
> I made the coupling and later the Dynamic process
>
> 1) In the initial 40ns, my ligand moves away from the binding site and
> consequently from the enzyme.
>
> What can I do to solve this problem?
>
> 2) When preparing the system in tleap, I notice that a Na+ is placed very
> close to my ligand and remains there during the entire simulation time, is
> this a problem? if yes how to solve?
>
> follow the image
>
> thanks
>
> --
> Prof Dr Renato Costa
> Instituto Federal do Pará - IFPA
> Grupo de Modelagem Molecular - UFPA
> Tel.+55 91 985484622
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 10 2022 - 10:30:03 PST
