GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question:
I am using gmx x2top to generate a topology file from a gro file. It doesn’t recognize some of the water and Cl atoms in the gro file. This gro file has a metal site, so that is why I want to use amber99sb.ff force-field. I think I need the amber99sb.ff force-field file or directory to manually specified the type of ions and water associated with the amber99sb.ff force-field.
Hi, you can download AmberTools (AmberTools24) and use xleap to generate the topology using the Amber force field of your choice. Then, you can convert the files into GROMACS format.
Also, I think it’s better to update your GROMACS version. The 2021 release is old, go for 2024.5 instead.
All the good luck.