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-
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.