Syntax Error in a forcefield.itp

User discussions
1

GROMACS version: 2018.3
GROMACS modification: No

I am running simulations with 6 copies of the same peptides to create a hexamer.

When I try to make a .tpr file to add ions to the system by gmx grompp -f ions.mdp -c cubic.gro -p topol.top -o ion.tpr, I get the following error: (I am using CHARM36m FF)

Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
‘1 2 yes 1.0 1.0’
Found a second defaults directive.

I got no such error when I ran simulations for just a monomer. Do you have any idea about what might be the problem with the forcefield file? Thank you.

2

Hi,
it looks like that you include twice the CHARMM force field. you can check your topology file (topol.top). Going from1 peptide to 6 peptide the main change is in the [ molecules ] part of the topol.top.
Best regards
Alessandra

3

Hi,

Thank you for the reply! I looked through the .itp files for all the six peptides, and found out that there were lines for forcefield.itp. I removed them and it works fine now.

Thank you,
Joseph

4

I am running simulations for protein and ligand. I have the same error. Can you guide me?

Thank you