[gmx-users] QM-MM (sai manohar)

[Groenhof, Gerrit]

Hi,

Unfortunately,  for this to work
you need to have both heme and protein in one topology. 

best,

gerrit

Tidings and a good day.

Hi,

I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, there's a small issue in this route. How do we incorporate the
dummy if the link we are pursuing is between the protein and the Heme that
are processed into two separate .top files in the first gmx step of
protein_proc.gro?

Any guidance in this direction would be extremely helpful.


Thank you.