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

[Dawid das]

Hi,

So does it mean that I need to change definition of each of my residues so
that they do not contain the carbonyl C and O atoms
for instance but instead the are bonded to the ACE "residue"?

Best wishes,
Dawid Grabarek

2016-02-02 16:17 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> 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.
>
> Mark
>
> 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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