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...@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)? > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
