You can change the protonation state of amino acids with pdb2gmx -inter option. It will ask you the protonation state of every AA. You could also start with a tool like propka in order to know which ones are protonated.
Best regards, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-28 9:18 GMT+02:00 Atila Petrosian <[email protected]>: > Dear Gromacs users, > > I want to study MD simulation of my protein in an special pH (2). > > I want to investigate partially unfolding in this protein. > > How to set charge of aminoacids in pdb file, prior to start MD? > > Any help will highly appreciated. > > Best > -- > 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 [email protected]. > -- 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 [email protected].
