Proper Procedure to generate GROOMAC input files from NMR structure

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No

Hy everyone, I’m a GROOMACS newcomer.

I want to perform some MD simulations of a protein that has been resolved by NMR spectroscopy (thus it has multiple structure models).
Do you know which is the proper processing workflow to prepare the NMR-derived PDB structure for GROOMACS?

Any advice would be welcome!

Regards,
Riccardo

2

I think the most common way is to select one representative model from the PDB file. To do that, just make a copy of the PDB file and delete the other models from it.

3

Thank you for your explanation! ATB!