Error: No default Proper Dih. types

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No
Conditions: no
Force Field: Gromos 54a7
Box type: Octahedron
Distance from edges of box: d = 1.3

How do I resolve the error notification “No default Proper Dih. types”.
Error message:
ERROR 1 [file topol.top, line 58797]:
No default Proper Dih. types

ERROR 2 [file topol.top, line 58798]:
No default Proper Dih. types

ERROR 3 [file topol.top, line 66096]:
No default Proper Dih. types

As a new user, I can not attach files. The protein that I was simulating was download from Alpha Fold. I removed amino acids 1119 to 1151 using pymol to reduce the size of the box.

Note: Disulfide bond between CYS-49 and CYS-1023

List of commands used:

gmx pdb2gmx -f Q5T5C0.pdb -o prot.gro -water spce -ignh -ter -ss

gmx editconf -f prot.gro -bt octahedron -d 1.25 -o prot_box.gro

gmx editconf -f prot_box.gro -o cent_prot.gro -center 8.6985 8.201 7.902

gmx solvate -cp cent_prot.gro -cs spc216.gro -p -o prot_wat.gro

  1. This is the command that created the error message:
    gmx grompp -f ions.mdp -c prot_wat.gro -r prot_wat.gro -p -o b4ions.tpr -maxwarn -1

ions.mdp file content:
; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary

2

Hi,

I guess the problem is that dihedral angles are not properly defined in the directive [ dihedral ] in the topology file. You can check how the lines

58797
58798
66096

looks like. Here you find information on the correct format https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table

I have noticed that you use also -maxwarn -1. It is usually good to resolve the warning before running, if possible.

\Alessandra