[gmx-users] question

[Andrew Bostick]

In fact, I want to make an isopeptide bond.

On Mon, May 11, 2015 at 11:04 PM, Andrew Bostick <andrew.bostick1 at gmail.com>
wrote:

> Dear gromacs users
>
> I have experience in MD simulation of protein and peptides by gromos force
> field.
>
> Now I am working on a new project in which I should connect two peptides
> (based on experimental data) to obtain one new peptide. This connection is
> as follows:
>
> CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from
> peptide 2.
>
> 1) How to make this connection (which software) to gromacs recognize this
> new state.
>
> 2) Should I need to change force field parameters?
>
> 3) Should I define new residue containing Glu-Lys?
>
> Any help will highly appreciated.
>