[AMBER] Costant ph simulation for Small molecules

From: Stefano Motta <stefano.motta.unimib.it>
Date: Fri, 7 Jun 2019 11:22:23 +0200

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).
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Received on Fri Jun 07 2019 - 02:30:02 PDT