GROMACS version: 2020.1
GROMACS modification: No
I am trying to set up a system that has a docked complex, the two molecules have been given the same chain ID and separated by a TER. Upon grompp, I get these errors:
Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘ns_type’ NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -1567179186 Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations ERROR 1 [file topol_Protein_chain_A.itp, line 57855]: No default U-B types ERROR 2 [file topol_Protein_chain_A.itp, line 58381]: No default U-B types ERROR 3 [file topol_Protein_chain_A.itp, line 58462]: No default U-B types ERROR 4 [file topol_Protein_chain_A.itp, line 81335]: No default Proper Dih. types ERROR 5 [file topol_Protein_chain_A.itp, line 81336]: No default Proper Dih. types ERROR 6 [file topol_Protein_chain_A.itp, line 81337]: No default Proper Dih. types ERROR 7 [file topol_Protein_chain_A.itp, line 81339]: No default Proper Dih. types ERROR 8 [file topol_Protein_chain_A.itp, line 82122]: No default Proper Dih. types ERROR 9 [file topol_Protein_chain_A.itp, line 82123]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’ Excluding 3 bonded neighbours molecule type ‘Protein_chain_A2’ Excluding 2 bonded neighbours molecule type ‘SOL’ NOTE 2 [file topol.top, line 48]: System has non-zero total charge: 10.000000 Total charge should normally be an integer. See Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation for discussion on how close it should be to an integer.
I have checked the .itp file, there no fractional charge, qtot is integral value. Also, I am not sure how to go about incorporating the parameters (‘No default U-B types’, ‘No default Proper Dih. types’)?
I am using the same ions.mdp file as this: http://www.mdtutorials.com/gmx/complex/Files/ions.mdp
Many thanks!