GROMACS version:2020
GROMACS modification: No
Here post your question Hello everyone from the Gromacs forum,
I’m currently working on simulating the kinetics of the P450 detoxifying enzyme heme complex in its role of detoxifying pesticides, but I’ve encountered some challenges in the initial steps. To begin with, I used Autodock to dock the heme group onto my protein model, and it forms a covalent bond with cysteine at position 441. I’m now wondering whether I need to separate the protein from the heme group to generate the topology files. If they are to be separated, how should I incorporate the covalent bonding part after generating the topologies individually? Conversely, if they are not to be separated, how can I properly describe the covalent bond in the topology? I’ve been utilizing the Gromos54a7 force field, but it seems to be inadequate for accurately describing the heme binding portion.
I would greatly appreciate any guidance you could provide.
Thank you very much.