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

[Dawid das]

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