[gmx-users] KALP 15 in model membrane

[Negar Parvizi]

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