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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
