Hi Gromacs Users, Just some background - I am doing FEP to determine the difference in binding free energy between two ligands (state A and state B) wherein state A has an isopropyl ether group and state B has a methyl ether group in its place. In other words I am transmuting the isopropyl group into a methyl group.
I am using a united atom topology file for my ligands and the GROMOS 96 forcefield. Ligand topologies come from the ATB. The difference in dG between these two states should be +7.04, from literature. I am not currently getting this value, not even within an RMSD of 10 kJ/mol. In transfiguring the isopropyl (state A) into the methyl moiety (state B), I have set the two CH3 and one H groups from state A into DUM atom types in state B, and likewise transfigured the central carbon of the isopropyl group, a C atom type, into a CH3 atom type. I have re-adjusted the charges on every state B atom for the state B ligand where necessary. My question is this - how do I state that the [ dihedral ] angles, [ angle ] and [ bonds ] from the CH3, CH3 and H atom types annihilated, no longer exist in State B, under the [ dihedral ], [ angle ] and [ bonds ] sub-headings? I have consulted the gromacs manual (section 5.7.4), but the table (table 5.6) and information included do not answer my question. Or the table (table 5.6) might have the information I need, but it is unclear what the table is saying. The example provided is also too simplistic (propanol to pentane) and I need to know what to do in my case. I've been told that even non-interacting atoms can contribute energy by virtue of their rotation so any advice on what to do would be greatly appreciated. Please let me know if you need more information. Kind regards, Billy -- 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.