GROMACS version: 2024
GROMACS modification: No
I have a pipeline for running MD simulations via Gromacs but encounter issues when preparing the simulation for various structures and complexes that contain nucleotides.
The step that fails is almost always:
gmx pdb2gmx -f input.pdb -o input_processed.pdb -water tip3p -ignh -missing
And the issue as far as I know is due to discrepancies between the expected structure at the termini of the nucleotides according to the force fields and the actual structure.
I’m wondering if there are any automatic pipelines or tools that can be used to prepare said structures ahead of time for my own pipeline.
Thanks in advance!