Dihedral error in protein in gromacs version 2021

User discussions
1

GROMACS version: 2021
GROMACS modification: No

While runing ion adding step I am reciving following error:

Blockquote

gmx grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr -maxwarn 2

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 -1763188889

Generated 168 of the 1653 non-bonded parameter combinations

ERROR 1 [file topol.top, line 26053]:
No default Proper Dih. types

ERROR 2 [file topol.top, line 26284]:
No default Proper Dih. types

ERROR 3 [file topol.top, line 26285]:
No default Proper Dih. types

Blockquote

Thank you in advance

2

People can help you more if you provide more information about your system. For example, what proteins or molecules do you have in your topology file? Did you create the topology file yourself for a molecule? Even posting parts of your .top file that produces the errors can be helpful for debugging.

Without more info, the error says: dihedral angles in your system are not defined right or are missing.

3

I didnt prepared a topology file by myself, I used a crystal structure monomer protien with 4 copper atoms.