How do I solve this error in GROMACS? (invalid order for the directive defaults)?

04 April 2019 1 8K Report

I wanted to run 10ns protein-ligand complex simulation.But I am not able to proceed next due to some fatal error.

Ligand (iso) parameter file iso.prmtop and iso.imprcd were generated through antechamber tool from amber library. Then both files were converted to iso.gro and iso.itp by using a amber script (script. Py).

By running this command ,

"gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr" I got error like

Fatal error:

syntax error - File iso.itp, line 17

Last line read:

'[ defaults ]'

invalid order for the directive defaults

Ehsan Shahini

Hi Sai,

You need to define atomtypes "only once" in your topol and put them all in the [ atomtypes ] of your first itp or topol.top. The error probably is because you have defined atom types two times in every itp files.

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