Fatal error: Invalid angle type 0

User discussions
1

GROMACS version: 2022.1
GROMACS modification: Yes/No
I’m using AMBER ff14SB force field and having some issues to make grompp command to add ions to the system as follows (.top and mdp files attached):

gmx grompp -f ions.mdp -c delta_RBD_solv.gro -p topol.top -o ions.tpr

getting the error:

                  :-) GROMACS - gmx grompp, 2022.1 (-:

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

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.

Program: gmx grompp, version 2022.1
Source file: src/gromacs/gmxpreprocess/topdirs.cpp (line 134)

Fatal error:
Invalid angle type 0

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

Any suggestions on how this error can be resolved?
Thanks by advance

ions.mdp (1.0 KB)

topol.top (812.1 KB)

2

Hi,
One source of this type of error can be that an angle is wrongly (or not) defined in the topology file. Did you get any warning or message concerning the angle when you have generated the topology using gmx pdb2gmx.

\Alessandra

3

Hi Alessandra,
Sorry for this delayed reply. I did have those kinds of problems, but I managed to solve the issue using tleap of AmberTools. It helped me translate the PDB for Amber forcefield.

Thankful for your response!