RNA structure simulation through Gromacs

General Topics in Molecular Dynamics
1

Hello Everyone!!

I am working on RNA structure simulation but I got an error on first step to create topology file through this command “gmx pdb2gmx -f S_000001.pdb -o S_00000_proc.gro -ignh” its showing

FATAL error: Fatal error:
Residue 1 named A of a molecule in the input file was mapped to an entry in the topology database, but the atom O5’ used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed

I have checked online for this error and could not find how to solve this… Kindly suggest me what to do

For Force field I have choose Amber99 (4th option)

For water model TIP3P

PFA, the picture of error

Screenshot from 2022-12-23 15-20-43
Screenshot from 2022-12-23 15-20-431920×1080 255 KB

Kindly suggest me how to solve this topology error

2

Hi @attaka ,
It would be better if you posted on GROMACS Forum
And this is due to missing atoms you have in your structure file or you have built your initial structure from some server where the naming has been messed up and does not matches with th e rtp entry of your force field.