Hi Which of the following is the correct method to prepare a protein for docking and then for protein-ligand complex MD simulation?
1. Do an MD simulation of protein for 100 ns and use the structure of protein at 100 ns to do the protein-ligand MD simulation. 2. Do an energy minimization of protein (like 5 ns) and use that structure for MD simulation of protein-ligand complex. Kindly let me know Thanks -- 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 [email protected].
