Dear all, I am trying to run a simulation of protein docked with ligands of interest. I have used autodock vina for the docking. Do i need to convert the receptor.pdbqt to receptor.pdb before proceeding? Do i need to add missing hydrogens in this step?
Also the protein of interest has four co-factors in the following order: (Co-factor A x 4no.s) HEM (Heme) Co-factor B. GROMOS identifies HEM. My doubt is weather I can retain the HEME group with protein and add the co-factor.gro files (obtained from ATB server) at a later stage or is it better to delete all the co-factors and add them together. Thanks in advance. -- Regards, Prasanth. -- 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.
