ERROR 1 [file topol.top, line 62]: No such moleculetype CL

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hi,

I am trying to run a heterodimer-ligand simulation. I am stuck at energy minimisation where running “gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr” gives me the fatal error: “ERROR 1 [file topol.top, line 62]:
No such moleculetype CL”.

The system seemed to solvate fine: “Replacing solvent molecule 1415 (atom 8369) with CL”

My topol file is:
"
; Include forcefield parameters
#include “./charmm36-jul2021.ff/forcefield.itp”

; Include ligand parameters
#include “vrx.prm”

; Include chain topologies
#include “topol_Protein_chain_C.itp”
#include “topol_Protein_chain_D.itp”

; Include Position restraint file
#ifdef POSRES
#include “posre_Protein_chain_C.itp”
#include “posre_Protein_chain_D.itp”
#endif

; Include ligand topology
#include “vrx.itp”

; Include water topology
#include “./charmm36-jul2021.ff/tip3p.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “./charmm36-jul2021.ff/ions.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_C 1
Protein_chain_D 1
VRX 1
SOL 14922
CL 1
"

Any ideas how to solve this issue?

Thanks

2

EDIT

My mistake, I checked ions.itp and it’s CLA rather than CL.

3

You can check charmm36-jul2021.ff/forcefield folder in your MD directory and see what symbol was used for representation of CL. In the new version of this script, the developer used SOD for Na and CLA for CL. You can also consider -maxwarn command in your commandline to suppress the warning errors you might see.

4

This seems like a common error.
I remember seeing it somewhere: