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

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 wrote: > Dear Gromacs Experts, > > I would like

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

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 : > Hi,

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

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