Constraints: How can I define bonds as H bonds

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Dear Gromacs User Forum,

Grompp gives me the following note when I input an .mdp file with the option “constraints=h-bonds”:

Screenshot from 2020-07-29 20-43-05

I am confident that my .mdp constraints options are correct.

But: For my simulation of DNA on diamond, I had to extend the Amber99/parmbsc1 Force Field with some parameters from the Generalized Amber Force Field. Among the added parameters were some H bonds, with H atoms called “NH” (for the surface functionalization of the diamond). I think that grompp does not turn these H bonds into constraints because it does not recognize them as H bonds.

Will it help if I rename the “NH” atoms to “HN”?

Or, alternatively:

The Force Field directory contains a file called “aminoacids.arn” with entries like:

; atom renaming specification
; residue gromacs forcefield
NALA H H1
NGLY H H1
NSER H H1
NTHR H H1
NLEU H H1
NILE H H1
NVAL H H1
…

Will it help if I add entries for the “NH” atom into this file?

Thank you for your patience.
I am grateful for any help.

Best Regards,
Stefan

2

The first character of the atom name must be H. Many GROMACS tools make this assumption (as it is standard practice for nomenclature basically throughout the simulation community), so make your life easy and use HN instead of NH.

1 Like
3

Thank you! :)