I suggest check for the appropriate binding pocket. See whether the ligand relocates at some other point in protein or keep to stay away. Also check for the quality of the topology generated.
On Wed, Aug 16, 2017 at 10:11 AM, <za...@tezu.ernet.in> wrote: > Hii Everyone > > I had performed a 100ns protein-ligand (docked complex) simulation with > gromacs 5.1.4. > > The ligand in my case is hydrogen peroxide. > > I have removed the PBC effect and centered the protein. > > I have used the following commands: > > gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc > > gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc > > I am analyzing the average distance between the protein and the ligand. I > am getting a value of 3.2nm which is too high. > > Also in the out_1.xtc, after 10ns itself the ligand is moving all around > the protein. > > Unable to understand why its happening!! > > Please suggest. > > Thank You > > Regards > > Z. Hazarika > Research Scholar > Tezpur University > Tezpur, India > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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 Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.
