[gmx-users] KALP 15 in model membrane

Armin Solemanifar armin.solemanifar at gmail.com
Tue Feb 13 00:44:35 CET 2018


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.


On Mon, Feb 12, 2018 at 9:39 PM, Negar Parvizi <negar.parvizi at yahoo.com>

> 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
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