GROMACS version: GROMACS/2024.3-cpeAMD-24.03-rocm (2024.3, MPI)
GROMACS modification: No
I am having troubles simulating a dimer structure of my protein.
The monomer simulations run perfectly, and running the simulation of the monomer interacting with DNA run perfectly as well, but when I attempt to simulate a dimer of the structure, I get the error message:
gmx_mpi editconf -f model.gro -d 0.8 -bt dodecahedron -o box.gro
ERROR 1 [file topol_Protein_chain_A.itp, line 54193]:
No default Per. Imp. Dih. types
ERROR 2 [file topol_Protein_chain_A.itp, line 54497]:
No default Per. Imp. Dih. types
ERROR 3 [file topol_Protein_chain_B.itp, line 54193]:
No default Per. Imp. Dih. types
ERROR 4 [file topol_Protein_chain_B.itp, line 54497]:
No default Per. Imp. Dih. types
How can I check this issue? Is there possibly something wrong with my PDB file? Where do I check the PDB to make sure the structures are coherent?
Here is the forcefield, just in case:
1: OL15 nucleic (Zgarbova et al., J. Chem. Theory Comput. 11, 5723-36, 2015
Thanks so much ahead of time,
M.