[gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 2 16:17:33 CET 2016


Generally one would use acetyl or N-methylamine capping groups respectively
for N and C termini of cleaved peptide bonds. These are often called ACE
and NME in .rtp files.


On Tue, Feb 2, 2016 at 2:58 PM Dawid das <addiw7 at googlemail.com> wrote:

> Dear Gromacs Experts,
> I would like to perform MD simulation of a system consisting of few amino
> acids
> cut out of the protein. The thing is that I break some peptide bonds and I
> add methyl
> groups in this place. Now I am missing charmm22 parameters for proper
> bonds.
> Could you give me a tip on getting missing parameters quickly? Which should
> I use?
> Or maybe there are parameters for cases as the one I am talking about.
> Best wishes,
> Dawid Grabarek
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