# Covalent binding in GROMACS

**URL:** <https://gromacs.bioexcel.eu/t/covalent-binding-in-gromacs/1914>\
**Category:** User discussions\
**Created:** [April 7, 2021, 4:14pm UTC](https://gromacs.bioexcel.eu/t/covalent-binding-in-gromacs/1914 "2021-04-07T16:14:42Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![IlseF](https://avatars.discourse-cdn.com/v4/letter/i/c5a1d2/32.png) [@IlseF](https://gromacs.bioexcel.eu/u/IlseF)\
**Post date:** [April 7, 2021, 4:14pm UTC](https://gromacs.bioexcel.eu/t/covalent-binding-in-gromacs/1914/1 "2021-04-07T16:14:42Z")

</div>

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!

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 8, 2021, 1:00pm UTC](https://gromacs.bioexcel.eu/t/covalent-binding-in-gromacs/1914/2 "2021-04-08T13:00:17Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![IlseF](https://avatars.discourse-cdn.com/v4/letter/i/c5a1d2/32.png) [@IlseF](https://gromacs.bioexcel.eu/u/IlseF)\
**Post date:** [May 17, 2021, 10:19am UTC](https://gromacs.bioexcel.eu/t/covalent-binding-in-gromacs/1914/3 "2021-05-17T10:19:15Z")

</div>

Thank you Justin,

I tried to write a .rtp file with a template ([rtp file format](https://manual.gromacs.org/archive/5.0/online/rtp.html)), 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