GROMACS version: 2022.2
GROMACS modification: Yes/No
Hi everyone, I need to run an MD simulation for a protein with copper ions inside and I have a question regarding the choice of the force field. I would like to use amber ff but the ones natively present in Gromacs it seems to me that are without parameters for Cu2+. Does exist an amber ff suitable for MDS with copper ions? And is there the possibility to download it and add it to gromacs?
Thank you
Hi,
You can find atom type CU in the atomtypes.atp and ffnonbonded.itp files in the all amber force field directories in GMXDATA/top. In each of force field directory you find also a forcefield.doc file that tell you the informatiom on how the Amber port for GROMACS was generated.
Here you can find the ion parameters compatible with AMBER force field
https://ambermd.org/AmberModels_ions.php
I hope cross-checking those information, you could understand if the implemented CU parameter is suitable for your case.
Kind regards
\Alessandra