Problem while reading RNA.rtp in latest OPLS force field

User discussions
1

GROMACS version: 2019.6
GROMACS modification: Yes/No

Hi all,
I have a problem while trying to generate nucleic.gro file by reading OPLS-AAM_for_Gromacs/oplsaam.ff files for RNA molecule. The residue and atom names are fine.
I am using OPLS force field files downloaded from here: GitHub - leelasd/OPLS-AAM_for_Gromacs: Gromacs Implementation of OPLS-AAM Force field

the command I used:

gmx pdb2gmx -f nucleic.pdb -ff OPLS-AAM_for_Gromacs -o nucleic.gro -ignh -ter

However, I am facing the error about ‘P’ atom as shown below.

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2019.6
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 164)

Fatal error:
Atom type oplsm_440 (residue RA) not found in atomtype database

the atom type “oplsm_440” is present in the database. I had checked PDB file format and other necessary things like editing rna.rtp file in gromacs format. However, I could not find the origin of the error.

I guess formating of rna.rtp file is issue, but I am not sure. Could anyone please suggest solution?

Thanks.

2

Hi,
gmx pdb2gmx lists all the residues database files at the begin of the standard output. You could cross check that these files are rtp, hdb, and tbd file that you want that pdb2gmx want to use.

You could also check that oplsm_440 atomtype is properly defined in ffnonbonded.itp and ffnonbonded_new.itp

Otherwise, you could contact the author of the repo.

\Alessandra