Hi, The force you assigned for position restrain may not be enough to hold the ligand in the proper position. If u follow the gromacs tutorial ...the simulation method is not wrong.
On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH <drrahulsur...@gmail.com wrote: > Hi Users. > > A basic clarification on protein and small molecule interaction. > > I have a docked complex of a protein-ligand (to accept, the docking score > is too low). On simulation, even after applying position restraint, I find > the ligand moving around the protein. Is this because there is any error in > the simulation method or it might be due to low interaction between the > ligand and protien? any suggestions to understand this problem? > > Thank you > > -- > *Regards,* > *Rahul * > -- > 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. > -- 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.