# Regarding my protein-dna complex molecular dynamics error **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [December 16, 2024, 5:36am UTC](https://gromacs.bioexcel.eu/t/regarding-my-protein-dna-complex-molecular-dynamics-error/10827 "2024-12-16T05:36:44Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Kirtiman07](https://avatars.discourse-cdn.com/v4/letter/k/ce7236/32.png) [@Kirtiman07](https://gromacs.bioexcel.eu/u/Kirtiman07)\ **Post date:** [December 16, 2024, 5:36am UTC](https://gromacs.bioexcel.eu/t/regarding-my-protein-dna-complex-molecular-dynamics-error/10827/1 "2024-12-16T05:36:44Z")
GROMACS version: GROMACS modification: Yes/No Here post your question when i start the simulation with the help of gmx pdb2gmx -f -o1.gro -p 1.top -water spce then select the forcefield i choose the charmm27 all atom and the fatal error coming. “Residue 443 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom OG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.” ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 16, 2024, 12:08pm UTC](https://gromacs.bioexcel.eu/t/regarding-my-protein-dna-complex-molecular-dynamics-error/10827/2 "2024-12-16T12:08:32Z")
You have at least one missing atom (Ser443 Oγ) that needs to be modeled in before the coordinates can be processed by `pdb2gmx`. ---
**Author:** ![Kirtiman07](https://avatars.discourse-cdn.com/v4/letter/k/ce7236/32.png) [@Kirtiman07](https://gromacs.bioexcel.eu/u/Kirtiman07)\ **Post date:** [December 16, 2024, 12:13pm UTC](https://gromacs.bioexcel.eu/t/regarding-my-protein-dna-complex-molecular-dynamics-error/10827/3 "2024-12-16T12:13:32Z")
Okay, understood. Thank You so much.