Hi Justin, Thank your very much for reply i have done both ways i also have backbone RMSD data so i will consider only this in my analysis.
Cheers, Sainitin On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/4/13 5:17 AM, Sainitin Donakonda wrote: > >> Hi all, >> >> I ran 20ns simulation on protein drug complex..now i want to check overall >> stability of this complex >> to acheive this i did following i supplied index file and choose >> Protein_Lig option for both least square fit and RMSD calculation..i used >> following command >> >> g_rms -f em.tpr (intital structure before production run) -s file.xtc >> (with >> out pbc) -n index.ndx -o complex.xvg >> >> >> is this correct way to determine overall stability of the complex ? or >> should i use only back bone of protein? >> >> > Using the whole complex probably obscures detail. Using the backbone or > Calpha atoms is much more common, because it gives you some insight into > the changes within the fold of the protein. I guess it all depends on how > you define "stability" and what you want to measure, but if you're trying > to assess the stability of the protein's structure, I wouldn't measure it > like you're doing. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > 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