What functional significance does it have, if any? --- According to my knowledge this reside is present in binding site.. and forms some hydrogen bonds with ligand
What is the residue? -- *Glutamic Acid* What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? --* I measured Just C-alpha atoms.* Let me know On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/9/13 3:29 PM, Sainitin Donakonda wrote: > >> Hi all, >> >> I recently performed MD simulation of protein - ligand complex..and >> analyzed its trajectory using RMSF tool in gromacs. >> >> This analysis revealed particular residue in binding site of protein >> showed >> quite high fluctuation around 0.30 nm but other residues were in range of >> 0.15 to 0.20 >> >> Can any body explain why this particular residue have high RMSF value in >> compared to other residues >> >> > Doubtful, at least not without considerably more information. What > functional significance does it have, if any? What is the residue? What > did you measure - RMSF of the whole residue, just the backbone, just > C-alpha, etc? > > Higher RMSF means the residue flops around more, i.e. your outcome > indicates that the residue deviates from the average position to a greater > extent than the other residues. Whether or not this actually means > anything at all depends on your knowledge of the nature of the > protein-ligand complex and the answers to the questions posed above. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
