VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Wed Oct 07 2020 - 13:44:43 CDT

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 AMBER (https://robinbetz.com/blog/2016/11/28/parameterizing-an-isopeptide-bond/) -- but Dr. Kohlmeyer pointed out in 2014 that converting AMBER parameters to CHARMM is not straightforward (https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23636.html). 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