Hi Gromacs users, I'm trying to calculate the relative binding free energy of a certain ligand when a leucine in the ligand binding site is mutated to glycine. The concept is simple but I have met some difficulties creating topology files for free energy calculation. I have two questions I wish you guys can help:
1. Let's say my protein have 200 residues and the leucine I want to mutate is in the middle (80 for example). When I tried to edit the topology of this protein, I found that since the number of atoms changed, I need to make lots of changes for bond, angle, and dihedral parameters. Is my feeling correct? 2. If my understanding is correct, I wish there are some existing scripts which can help people create topology file for mutational free energy calculation. I will highly appreciate if you guys tell me where I can find them. Thank you very much. Yi An Postdoctoral Research Associate UNC-Chapel Hill -- 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.
