From: Josh Vermaas (
Date: Wed Oct 07 2020 - 14:48:53 CDT

Hi Harper,

The first thing I'd check is to see if the DKAM patch is what you are
looking for (its in stream/prot/toppar_all36_prot_modify_res.str in a
standard CHARMM36 distribution), which based on the description in the file
is meant to describe the situation similar (ASP-LYS staple), and is a
blessed part of the CHARMM36 force field. You'd apply it via a patch to
your current protein. I like to use the DISU patch in the psfgen
userguide as the example syntax of how patches are applied to two residues,
keeping in mind that the order matters in your case (ASP/GLU first, then
the LYS). If it needs to be a Glu, the first step would be to check if it
exists somewhere else in the stream files (I don't know them by heart), or
do the changes by analogy.


On Wed, Oct 7, 2020 at 1:09 PM Smith, Harper E. <> wrote:

> Hi mailing list,
> I'd like to use CHARMM parameters to simulate a system containing a
> Glu-Lys isopeptide bond, but I am unsure how to generate the parameters.
> I have seen guides for parameterizing small molecules using FFTK, but is
> this appropriate for a covalent bond between two side chains?
> There is a guide by Robin Betz about making isopeptide bond parameters for
> -- but Dr. Kohlmeyer pointed out in 2014 that converting AMBER parameters
> to CHARMM is not straightforward (
> Is
> this still true?
> In your opinion, could you give me a sense of the difficulty of this
> problem? Can a non-expert like me generate publication-quality parameters
> for this covalent modification?
> Best,
> Harper Smith