On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote:
> 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. > Thank you. I am sure, I haven't changed any step from the tutorial. Is there any better option to hold the ligand and protein together? Thank you Mr. Das > > 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. > -- *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.