[gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme parameters in the mol2 and frcmod file format. I know that I can generate .itp files containing the parameters, which I can later add to my .top file. However, it would be much easier to use pdb2gmx directly without stripping the heme and the cysteine binding the heme and later manually add it again. I added the cysteine to the standard amber force field. However, before adding the heme manually I wanted to know if there is a way to load an itp file while executing pdb2gmx?

How would you add the information from the cysteine in mol2 format and the heme in mol2/frcmod format to amber in gromacs?

Thank you very much,

Max