Re: [AMBER] Costant ph simulation for Small molecules

From: Marcos Serrou do Amaral <marcossamaral.gmail.com> Date: Fri, 7 Jun 2019 06:31:12 -0400

---
Marcos S.A.
On Fri, Jun 7, 2019 at 5:22 AM Stefano Motta <stefano.motta.unimib.it>
wrote:
> Dear AMBER users,
>
> I was wondering if there is a way to perform constant pH simulations for
> small molecules, or if the only groups that can be protonated/deprotonated
> are protein/nucleic acid residues.
> What I would like to do is building parameters for a small molecule with
> GAFF, than adjust the parameters for constant pH simulation for a simple
> system (my small molecule in water) to reproduce the experimental pKa
> value, and finally run the simulation of a complex system (more than a
> small molecule and other molecules).
>
> Is this something that could be done?
> Thank you all in advance,
>
> Best wishes,
> Stefano
>
>
> --
> ________________________________________________________________
>
> Stefano Motta PhD
>
> Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
>
> Università degli Studi di Milano Bicocca
> Department of Earth and Environmental Sciences
>
> Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> _________________________________________________________________
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber