Protonation state of the amino acids are set during execution of pdb2gmx and you can choose yourself what their protonation state is using -inter or any of the other options if you don't want to go through all.
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 4 May 2020 at 02:59, azadeh kordzadeh <azadehkordza...@gmail.com> wrote: > Hi > I gave a topology of a protein with pdb2gmx command in next step I change > protonation some aminoacids but the topology didn't chage. How could I > create new topology? > I need to obtain topology protonated aminoacid from other servers? > Thanks > -- > 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. > -- 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.