Hi, Putting capping on the peptide/protein end affect the its polarity and you should check how it could affect your protein structure or whether you want it to be charged or not at the tails.
Cheers, Armin On Mon, Feb 12, 2018 at 9:39 PM, Negar Parvizi <negar.parv...@yahoo.com> wrote: > Dear all Gromacs usersI have started the tutorial on membrane protein, > provided by Justin ( KALP 15 in model membrane).Now I have two questions:1) > Why Justin adds the ACE and NH2 groups to the two ends of the peptide model? > The -ter option in pdb2 gmx command can add interactively the NH2 or NH3+ > , and COOH or COO- to the N and C terminies.What is the preference of ACE > over COO- or COOH? > 2) The next question is: How should I decide to add which of the mentioned > groups to the N or C terminies, when simulating the transmembrane protein?? > Thanks in advance for your timeNegar > -- > 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.