Covalent binding in GROMACS

User discussions
1

GROMACS version: 2021
GROMACS modification: No
Hello everyone,

Does anybody know how to create a topology for covalent bound ligands in GROMACS? Now I have created a 25 nanoseconds, but the covalent bond is not preserved and not visible despite I used a crystal structure with a visible covalent bond. My ligand contains a boron which is supposed to bind to the oxygen of a serine residue. Thanks in advance!

2

You need to create an .rtp entry for the species that defines all the bonded connections to the other residues in the molecule. What is “visible” using visualization software means nothing; those are just guesses by those programs based on atomic proximity. What matters is the topology, which governs the actual physics during the simulation.

1 Like
3

Thank you Justin,

I tried to write a .rtp file with a template (rtp file format), and I have some questions.

  1. Could you maybe check if I did it right? The file is attached below completely with some of my notes.

-START OF THE FILE -
[ bondedtypes ] ; mandatory
; bonds angles dihedrals impropers
1 1 1 2 ; mandatory

[ SER ] ; mandatory

[ atoms ] ; mandatory
; name type charge chargegroup
N N -0.280 0
H H 0.280 0
CA CH 0.000 1
C C 0.380 2
O O -0.380 2
CB CH2 0.000 1
CG CH2 0.000 1
OG O 0.000 0
B B xyz (from PDB?) chargegroup (from PDB?)

here do we need to place the other atoms of the ligand? (1)

[block of other atoms]

[ bonds ] ; optional -here we set up the covalent bond
;atom1 atom2 b0 kb
N H
N CA
CA C
C O
-C N

here do we need to place the other atoms of the ligand? (2)
[block of other atoms]

[ exclusions ] ; optional
;atom1 atom2

[ angles ] ; optional
;atom1 atom2 atom3 th0 cth → (what it is)
C(ligand) B CG

[ dihedrals ] ; optional
;atom1 atom2 atom3 atom4 phi0 cp mult

[ impropers ] ; optional
;atom1 atom2 atom3 atom4 q0 cq
N -C CA H
-C -CA N -O
-END OF THE FILE-

  1. When you mentioned “other residues” do you mean the entire block of atoms & bonds connections & angles that characterize that specific ligand I am studying? For example, in my case I have 31 atoms: is there any command generator which you can recommend me for getting e.g the charge/chargegroup of the atoms, the th0 of the angles and so on?

Thanks in advance