[ atomtypes ] error

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
I want to simulate two types of small molecules in the system, and each type there are multiple of them.
I created the files.itp for ligand1 and ligand2 Acpype Server server
The question I have is this: since there are two types of molecules, can I have two itp files for each molecule
When I used this command
gmx grompp -f em.mdp -c solv.pdb -p topol.top -o em.tpr -maxwarn 2
there was this error
Fatal error:
Syntax error - File lig2.itp, line 3
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

topol.top fill
; Include forcefield parameters
#include “charmm36-jul2021.ff/forcefield.itp”

; Include ligands topologies
#include “lig1.itp”
#include “lig2.itp”

; Include water topology
#include “charmm36-jul2021.ff/tip4p.itp” in water

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

[ system ]
; Name
PRO topology, generated by TopolGen in water

[ molecules ]
; Compound #mols
LIG1 1
LIG2 1

2

You cannot introduce atom types in different files, that violates topology hierarchy. All atom types have to be known before any [moleculetype] can be declared.

Also, AcPype is compatible with GAFF/AMBER so do not try to use those topologies with the CHARMM force field.

3

Thanks a lot for your help and patience @jalemkul