Yes Justin...i watched the dynamic structure carefully. As it is a transmembrane protein it is stringently moving. The dynamic movement of the structure seems fine. I used the backbone of protein for calculating Rmsd. I also want to know the ligand stability, for it i need to check the least square fit of ligand , right? On May 19, 2015 5:11 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > > On 5/19/15 6:29 AM, Priya Das wrote: > >> Dear all, >> >> While generating RMSD plots of protein in presence of ligand, i am getting >> a RMSD of around 4.5 Angstrom around 10 ns after which the system is >> almost >> stable. >> Is it an acceptable RMSD? >> What is the acceptable range for RMSD for structures? >> >> > There is no general rule, and a number without context is meaningless. > How did you calculate the RMSD - backbone? heavy atoms? all atoms? Does > your protein have a lot of variable loops, and did you consider these? Or > did you just consider structured parts of the protein? Did you include > termini? Did you watch the trajectory to see what's happening? > > -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. > -- 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.