hi i am working of protein ligand binding free energy calculation, i have seen some tutorials, like from alchemistry websites and from some paper works. i made ligand topology with acpype (amber.ff) and used pdb2gmx for protein topology, then i combined gro files to make a complex. now i dont know how to make complex topology. i already studies and used tutorials from Bevanlab but it doesnt provide info about how to include protein and ligand as one moleculetype. and also how should i get the dihedral, angle and distance restraints. i studied gromacs manual about this but it doesnt provide any direction. if anyone have some tutorial, kindly suggest. Thanks in advance
; distance restraints[ bonds ]; i j type r0A r1A r2A fcA r0B r1B r2B fcB 2143 1656 10 0.615 0.615 10.0 0.0 0.615 0.615 10.0 4184.000 [ angle_restraints ]; ai aj ak al type thA fcA multA thB fcB multB 1658 1656 2143 1656 1 92.14 0.0 1 92.14 41.840 1 1656 2143 2142 2143 1 107.4 0.0 1 107.4 41.840 1 [ dihedral_restraints ]; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 1668 1658 1656 2143 1 157.05 0.0 0.0 157.05 0.0 41.840 1658 1656 2143 2142 1 -129.56 0.0 0.0 -129.56 0.0 41.840 1656 2143 2142 2140 1 166.61 0.0 0.0 166.61 0.0 41.840 Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea. -- 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.
