Fatal error: There were 2 errors in input file(s)

GROMACS version: 2020.1
GROMACS modification: No
Here post your question : I found an error message like the one below after I tried the add ions step on my complex. (my .pdb protein was previously prepared to change the pH using Yasara). Can someone give me some advice? Thanks.

Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

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 -510674674
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file sin.itp, line 331]:
No default Proper Dih. types

ERROR 2 [file sin.itp, line 344]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘SIN’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 48771]:
System has non-zero total charge: -12.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.

There were 2 notes


Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There were 2 errors in input file(s)

You don’t have required parameter for molecule SIN

thanks for your response, may I know how to add the required parameters for the SIN molecule? thank you

Follow Protein_ligand tutorial. How did you parameterised SIN molecule?

I use CHARMM General Force Field server

You probably forgot to #include the associated parameter file. If there are new parameters for the ligand, the server generates them and our conversion utility writes them to a separate file. This is addressed in my tutorial: Protein-Ligand Complex