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 before posting!

* Can't post? Read

* For (un)subscribe requests visit or send a 
mail to

Reply via email to