Thank you. I got following when I analysed Ligand RMSD protein backbone as east square fit. Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7> Can you please comment why there's high fluctuation after like 23 ns? What could this mean?
Thanks Regards! On Sat, Oct 5, 2019 at 9:08 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/19 11:36 AM, Quin K wrote: > > OK thanks. > > What should I pick for least square fit in following instances for > example. > > *RMSD of* > > 1. protein backbone+ligand > > 2. protein backbone > > 3. lingad only > > I've already answered that. And again, it always depends on the question > you are asking. You want the change in a structure relative to > something. What is that something and how can you justify (to yourself > and your reviewers!) that choice? > > -Justin > > > On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 10/5/19 11:24 AM, Quin K wrote: > >>> Thank you! > >>> How important is the least square fit in these RMSD calculations? > >> Very; it determines how to interpret the result. > >> > >>> Or should I just pick system for least square fit all time? > >> You should never pick "System" for a fit. > >> > >> -Justin > >> > >>> On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>>> On 10/5/19 11:11 AM, Quin K wrote: > >>>>> To see if complex is stable and to see how it fluctuate in the > binding > >>>>> site. > >>>> Stability of the complex can mean multiple things. If you want to show > >>>> that the protein structure is stable in the presence of the ligand, > you > >>>> would compute the RMSD of the protein (probably backbone) and compare > >>>> the result against that of an apo simulation. If you want to show that > >>>> the complex is stable in terms of the association of the protein and > >>>> ligand, that's not something you do via RMSD; you compute distances, > >>>> angles, etc. related to the interactions of the protein that hold the > >>>> ligand in the active site. > >>>> > >>>> You need to define what "it" is in the context of fluctuations. > >>>> Fluctuation of the ligand in the binding can be computed by > calculating > >>>> RMSD of the ligand after a fit to the protein (to get relative > motion). > >>>> You can also do RMSF (e.g. of binding site residues, again to be > >>>> compared against apo data for context/control). > >>>> > >>>> -Justin > >>>> > >>>>> On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul <jalem...@vt.edu> > wrote: > >>>>> > >>>>>> On 10/5/19 10:53 AM, Quin K wrote: > >>>>>>> Hi, > >>>>>>> > >>>>>>> *What should I pick for RMSD analysis of protein ligand complex? * > >>>>>>> *What other analysis can be done for protein ligand complex? * > >>>>>>> Following are the options I have for least square fit and for RMSD > >>>>>>> calculation. > >>>>>>> MPPA is the ligand I used. > >>>>>>> Group 0 ( System) has 50085 elements > >>>>>>> Group 1 ( Protein) has 4590 elements > >>>>>>> Group 2 ( Protein-H) has 2307 elements > >>>>>>> Group 3 ( C-alpha) has 282 elements > >>>>>>> Group 4 ( Backbone) has 846 elements > >>>>>>> Group 5 ( MainChain) has 1127 elements > >>>>>>> Group 6 ( MainChain+Cb) has 1396 elements > >>>>>>> Group 7 ( MainChain+H) has 1399 elements > >>>>>>> Group 8 ( SideChain) has 3191 elements > >>>>>>> Group 9 ( SideChain-H) has 1180 elements > >>>>>>> Group 10 ( Prot-Masses) has 4590 elements > >>>>>>> Group 11 ( non-Protein) has 45495 elements > >>>>>>> Group 12 ( Other) has 31 elements > >>>>>>> Group 13 ( MPPA) has 31 elements > >>>>>>> Group 14 ( NA) has 2 elements > >>>>>>> Group 15 ( Water) has 45462 elements > >>>>>>> Group 16 ( SOL) has 45462 elements > >>>>>>> Group 17 ( non-Water) has 4623 elements > >>>>>>> Group 18 ( Ion) has 2 elements > >>>>>>> Group 19 ( MPPA) has 31 elements > >>>>>>> Group 20 ( NA) has 2 elements > >>>>>>> Group 21 ( Water_and_ions) has 45464 elements > >>>>>>> Group 22 ( Protein_MPPA) has 4621 elements > >>>>>>> > >>>>>>> Thanks & regards! > >>>>>> What is your objective in calculating RMSD? > >>>>>> > >>>>>> -Justin > >>>>>> > >>>>>> -- > >>>>>> ================================================== > >>>>>> > >>>>>> Justin A. Lemkul, Ph.D. > >>>>>> Assistant Professor > >>>>>> Office: 301 Fralin Hall > >>>>>> Lab: 303 Engel Hall > >>>>>> > >>>>>> Virginia Tech Department of Biochemistry > >>>>>> 340 West Campus Dr. > >>>>>> Blacksburg, VA 24061 > >>>>>> > >>>>>> jalem...@vt.edu | (540) 231-3129 > >>>>>> http://www.thelemkullab.com > >>>>>> > >>>>>> ================================================== > >>>>>> > >>>>>> -- > >>>>>> 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. > >>>>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> 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. > >>>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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? 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