Combining files from LigParGen

User discussions
1

GROMACS version:2021.1
GROMACS modification: No

Dear all,

I would like to apply the Lysozyme in Water tutorial from Lysozyme in Water to my own system (TFSI diluted in diglyme).
I have for both systems the results from LigParGen, the top file being different.

I can put the box around the salt and solvate it successfully. On the contrary, when using gmx grompp, I get:

Fatal error:
Syntax error - File TFSI.top, line 6
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes

What is the system expected to find here?
Comparing to the results from the tutorial it might be this:

; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”

[ moleculetype ]
; Name nrexcl
Protein_chain_A 3

Could anyone give me a hint here?

Thank you

Best regards,
MDG

2

All force field parameters have to be defined before they can be invoked in a [moleculetype] definition. If you have multiple topologies that introduce [atomtypes], then you need to combine these directives. See Common errors when using GROMACS — GROMACS 2021.1 documentation