[gmx-users] Protein atomic charges modeling question

Joe Jordan e.jjordan12 at gmail.com
Wed Apr 11 08:42:41 CEST 2018

Since molecular dynamics simulations are classical in nature, you, or the
forcefield you choose, must set the partial atomic charges. You must also
determine your desired protonation states based on the pH conditions you
want to simulate.

To actually answer your question, there are programs that calculate what
you want, but they are outside the scope of gromacs.

On Wed, Apr 11, 2018 at 2:24 AM, Thanh Le <thanh.q.le at sjsu.edu> wrote:

> Is there a program or algorithm for calculating atomic charges in protein
> R group amino acid residues in various conditions (ie ligand binding
> partners, solutions of various pH, hydrophobic pockets, etc)?
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Joe Jordan

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