Error while going for energy minimization

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1

GROMACS version: gmx_mpi version 2021.3

GROMACS modification: Yes/No
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I generated the topology for a dodecane molecule using the oplsaa forcefield. I entered the parameters by manually editing all the components into the local forcefield directory, like adding bond, angle and dihedral parameters into the ffbonded.itp folder. The topology was generated successfully using the pdb2gmx command but when I ran an energy minimization, I got this error.

ERROR 1 [file topol.top, line 206]:
No default Angle types

ERROR 2 [file topol.top, line 207]:
No default Angle types

ERROR 3 [file topol.top, line 214]:
No default Angle types

ERROR 4 [file topol.top, line 220]:
No default Angle types

ERROR 5 [file topol.top, line 226]:
No default Angle types

ERROR 6 [file topol.top, line 232]:
No default Angle types

ERROR 7 [file topol.top, line 238]:
No default Angle types

ERROR 8 [file topol.top, line 244]:
No default Angle types

ERROR 9 [file topol.top, line 250]:
No default Angle types

ERROR 10 [file topol.top, line 256]:
No default Angle types

ERROR 11 [file topol.top, line 278]:
No default Ryckaert-Bell. types

ERROR 12 [file topol.top, line 279]:
No default Ryckaert-Bell. types

what should I do?

2

Hi
An option is to add the missing values in the topology file (if they are available in force field you plan to use). I also suggest to have a look if pdbgmx was reporting some NOTE/WARNING that may help to understand what and why something is missing.
Regards
Alessandra

3

Thank you…yes there were a few angle parameters missing in the ffbonded.itp file. I corrected it

4

HI Gourav
how i can do that ?
from where i can get the parameters ?