No such molecule type LIG

User discussions
1

GROMACS version: 2023
GROMACS modification: Yes/No

In wsl (Ubuntu), I installed the new Gromacs v2023 version. It successfully runs the simulation of proteins in water, but when I run the simulation of the protein-ligand complex. It generates some errors. The common error is No such molecule type LIG. In the molecule section, I define the LIG.
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
SOL 23527

ERROR 1 [file topol.top, line 8889]:
No such moleculetype LIG

The .gro and .itp have same name LIG

cmd: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Example…
LIG.gro created by acpype (v: 2022.7.21)
29
1 LIG C 1 -0.263 0.071 -0.001
1 LIG C1 2 -0.264 -0.070 0.003
1 LIG C2 3 -0.145 -0.143 0.003
1 LIG C3 4 -0.028 -0.071 -0.002
1 LIG C4 5 -0.027 0.067 -0.004
1 LIG C5 6 -0.143 0.142 -0.003
1 LIG C6 7 0.113 0.109 -0.008
1 LIG O 8 0.152 0.224 0.001
1 LIG N 9 0.188 -0.005 -0.015
1 LIG C7 10 0.111 -0.118 -0.006

Did I miss something? Please help me.
Thanks in advance

2

Hi,
Do you get the error when you run gmx grompp?
Then, it looks like that program do not find the parameter information for the LIG in the topology file (and in all the file included in the topol.top). You can check if you provide such a information.
\Alessandra

3

hi, were you able to solve this?

4

Yes. I solved by correcting the file name. Actually i was using acpype for ligand topology. Acpype generate the file name by your file name and inside the file in header section it also includes original file name with extension. such as my file name is lig.pdb so it include it as lig.pdb.gro or lig.pdb.mol2.gro or lig.pdb.mol2.itp. You can check your ligand topology header line and in itp check both sections: atomtypes and molecules type. Name should be same everywhere.

For example. your molecule topology file name is lig.gro and lig.itp and atom coordinates name also a LIG then in every file, it should be a lig or LIG. And also check the same in nvt.mdp, npt.mdp and md.mdp.