From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Oct 07 2020 - 19:31:08 CDT

Sage advice!

You could also do what I do and hire chemists for your lab, but I appreciate that isn’t an option for everyone! ;)

More to the point, we’ve tried multiple times to write papers that distill the secret sauce for parametrization (as far as we understand it!) into a recipe-like form, but it never comes across as well as we imagine at the outset. Every problem is unique, and it’s only with a lot of experience that one starts to get the hang of things.

For your specific problem, looking at ASP and GLU in the C36 force field, the terminal side chain groups are almost the same, so it should be a straightforward adaptation of the DKAM patch that Josh mentions. You would just change “1CB” to “1CG” and “1CG” to “1CD" in the patch (if I am right - compare them very carefully yourself!).

Best,
JC

> On Oct 7, 2020, at 5:08 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>
>
> On Wed, Oct 7, 2020 at 4:53 PM Smith, Harper E. <smith.12510_at_buckeyemail.osu.edu <mailto:smith.12510_at_buckeyemail.osu.edu>> wrote:
> Hi Josh,
> Is there a more standard way to proceed for someone with weak chemical intuition?
>
> In my personal opinion, the best approach to this is to find an experienced collaborator. It used to be the common way back in the times when tools were less easy to use and information on how to use them was not as readily accessible to anyone as now.
>
> While it is much easier to get started now and do good work on straightforward projects, anything more complex has become more risky, since people don't go through an "apprenticeship" period anymore where they learn the "tricks of the trade" and about the non-obvious sources of errors that are known to experienced practitioners, but rarely put in writing (mostly because they are not really of the "do this, not that" category and thus not simple to write about).
>
> Axel.
>
>
> Best,
> Harper Smith
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0 <http://goo.gl/1wk0>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.