No default proper Dih. Types when forming ions.tpr

User discussions
1

GROMACS version: 2024.2
GROMACS modification: Yes/No
Forcefield:charmm36-jul2022

Hello Gromacs users:
I’m doing simulation on peptides contain D-form Proline (VAL-D-PRO-PRO), and I encounter errors when forming ions.tpr

gmx grompp -f ions.mdp -c S2H5D8MAX1_box_solvate.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 -1367515393

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

ERROR 1 [file topol_Protein_chain_A.itp, line 4582]:
No default Proper Dih. types
…

I check for topol_Protein_chain_A.itp file, and found it correspond to
C(VAL) N CPD1 C

Then i look for this parameter in ffbonded.itp and found this
C N CPD1 C 9 0.000000 3.347200 3 ;
So it seems like the parameter does exist, so I dont understand what’s wrong.
Any help will be appreciated!

Milo

2

Hi Milo,

Could you please state your problem more clearly?

Anyway, If you would like to add any parameters to .itp files manually you should introduce it first. Did you introduce CPD1 in your forcefield file?

For example, C is known usually as CT in the OPLS forcefield. So, you can define dihedral parameters related to C like:

N CT N O .......

I hope it will help.

3

hi Mr.eezayani:

Sorry, my first question may not have been very clear. I have made revisions.
My question is : grompp is complaining there is no dihedral type, but i check for ffbonded.itp, there is parameter there as i mention above.
And i believe CPD1 atomtype is already written in charmm forcefield.

Thanks!