Simulating protein-ligand-cofactor (Invalid order for directive atomtypes)

User discussions
1

GROMACS version: 5.2
GROMACS modification: No

Hello,

I am having a difficulty preparing a gromacs simulation system with a protein-cofactor-ligand system. No issue until the add ion stage, where I keep getting the famous

(

Fatal error:

Syntax error - File MOL_updated.itp, line 13

Last line read:

‘[ atomtypes ]’

Invalid order for directive atomtypes

) error.

I tried to follow up the tutorials and the online suggestions on how to solve this issue, but I could not. Please find the complex, cofactor (NADPH) and ligand (MOL) topology files attached, as well as the solvated complex gro.

I appreciate any suggestion,

This is the command I am running (gmx_mpi grompp -f ions.mdp -c solvated_complex.gro -p topol_complex_standalone.top -o ions.tpr -maxwarn 5)

Thanks,

Marawan

MOL_updated.txt (33.0 KB)
NDP.txt (39.9 KB)

2

solvated_complex.txt (2.2 MB)
topol_complex.top (1.0 MB)

3

Firstly, atom types must come before all atoms entries. This means that you cannot have atom types defined in both MOL_updated.itp and in NDP.itp. Make a separate .itp file containing only the atom types blocks from those two files (and remove it from those files). Include that file before the #include "NDP.itp" line in the .top file.

Secondly, in the NDP.itp file you should make sure that the atoms block comes after the moleculetype block.