Dear Justin First I apologise for the error I had made in my previous mail. It's during production.
I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/1/17 8:59 AM, RAHUL SURESH wrote: > > I followed the complex simulation tutorial. Minimisation for 2ns > > > > FYI there is no time during energy minimization, so you did not do "2 ns" > of > minimization. > > > I used auto dock to dock ligand with protein. During simulation I find > the > > ligand out of protein. Is that usual? > > > > This is probably a periodicity effect. There's no way during the course of > minimization that a ligand-protein complex can completely dissociate. Use > trjconv to make sure you've properly re-imaged the system. A simple > recentering > should do it. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.