Hi there, Because the bond and angle parameters are harmonic terms in many forcefields, my understanding is that they should cancel out during a closed thermodynamic cycle. So you will not need state B parameters for those terms.
However, you will need to state state B terms for proper and improper dihedrals though. Refer to the papers by Boresch, et al. from 1999. Cheers, Billy On 27 September 2016 at 03:34, Rui Neves <rppne...@gmail.com> wrote: > Hi Gromacs users, > > I am trying to determine a relative binding free-energy of two hypothetical > ligands (A -> B). > > To do this, I must indicate a typeB for the atomtypes in B. > Once this is done, do I have to explicitly include the bonded parameters > for the B state, if I started by loading all the parameters of the force > field that parameterizes both ligands? > > Thank you for any help, > > Regards, > > Rui Neves > -- > 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. > -- Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon *LinkedIn Profile <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button> **|* +61420 382 557 Monash Institute for Pharmaceutical Sciences ( *MIPS* ) Royal Parade, Parkville, 3052 -- 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.