No default U-B error with charmm36 force field

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes

Dear GROMACS users.
As I would like to use the charmm36 force field, I followed tutorial written by Justin. And there was another version of charmm36 force field that I used, named charmm36-mar2019.ff’.
However when I run genion step, there was errors that I have never met:
ERROR 1 [file lig.itp, line 437]:
No default U-B types

ERROR 2 [file lig.itp, line 451]:
  No default U-B types


ERROR 3 [file lig.itp, line 630]:
  No default Proper Dih. types


ERROR 4 [file lig.itp, line 633]:
  No default Proper Dih. types


ERROR 5 [file lig.itp, line 636]:
  No default Proper Dih. types


ERROR 6 [file lig.itp, line 639]:
  No default Proper Dih. types


ERROR 7 [file lig.itp, line 648]:
  No default Proper Dih. types

Is there any point what I’m missing or what I have to check???
How can I solve this problem?

Best regards,
Jinyoung

2

The ligand requires new parameters that should be provided by a file called lig.prm if you used our conversion script. That file needs to be #included at the top of the topology.

3

please check related lines such as 451for bonded parameter and other lines for Proper Dih. types
then add force field parameter in topology file.

4

I’ve already added lines at the top of topology file(topol.top) as below:

; Include ligand topology
#include "../LIGAND/lig.itp"

; Include ligand parameters
#include "../LIGAND/lig.prm"
5

Parameters required by the ligand have to be #included before the ligand topology. What you have now is a ligand topology that requires new parameters, and you’re only defining those parameters later. That won’t work.