You need to make one topology for your protein that includes all atoms that you want to treat with QM. If your QM region includes part of the protein and the ligand, you can most easily make one topology with the -merge option of pdb2gmx.
Gerrit Dear Gromacs Users, I am interested to know how to create a separate topology file for the QM atoms of a system. It would be of great help if somebody can explain this. For my QM system, I need to include the active site residues + ligand. -- *Best Regards* BM -- -- 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.
