Dear users, I add the following [ intermolecular_interactions ] section into the topology file of protein-ligand complex for free energy calculations. Unfortunately this setting doesn't provide me what I want in the decoupled state. The ligand in the decoupled state is very mobile compared to the coupled state. It means that the conformational sampling of the ligand in the decoupled state is quite different from the coupled state. That is not expected of course. Any suggestions as to why this might be?
Do you think that there is something wrong with the following settings, e.g. [ dihedrals ] part? [ intermolecular_interactions ] [ bonds ] ; ai aj type bA kA bB kB 1391 2615 6 0.654 0.0 0.654 4184.0 [ angles ] ; ai aj ak type thA fcA thB fcB 1393 1391 2615 1 88.8 0.0 88.8 41.84 1391 2615 2614 1 32.9 0.0 32.9 41.84 [ dihedrals ] ; ai aj ak al type thA fcA thB fcB 1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84 1393 1391 2615 2614 2 122.6 0.0 122.6 41.84 1391 2615 2614 2610 2 12.8 0.0 12.8 41.84 Should I use the following [ dihedral_restraints ] part instead of the above [ dihedrals ] part? [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 1410 1393 1391 2615 1 -159.7 0.0 0.0 -159.7 0.0 41.84 1393 1391 2615 2614 1 122.6 0.0 0.0 122.6 0.0 41.84 1393 1391 2615 2614 1 12.8 0.0 0.0 12.8 0.0 41.84 I think [ dihedral_restraints ] will be the same as [ dihedrals ] because the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are taken as 0 (zero), right? Thanks in advance -- Ahmet Yildirim -- 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.