Thank you Joao and Aman. I have noted the points you have suggested.
Do you think analyzing DSSP would help? Thanks, Neha On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "You can use various supporting tools from R language to debug your > trajectory but most third party software support NAMD and charmm format. > You can use VMD to convert the trajectory to dcd and use R language based > packages to read your trajectory" > > What? How is this useful or helpful? At most it confuses the OP even more. > > Also, the clustering analysis is unlikely to be what you want or need at > this stage. Why overcomplicate? One of the simplest ways to check that > there are conformational changes on a given set of atoms is by doing a RMSD > analysis using the folded structure as the reference. The RMSD is somewhat > degenerate, but should suffice for this purpose. You can use an index file > to restrict the RMSD analysis to a particular subset of your system (the > docking site, for example). > > You could look at the radius of gyration as well, Rg, as Aman Deep also > suggests. This can either be calculated on a subset of atoms or on the > entire protein. The latter could potentially be used to compare with the > experimental reference obtained by SAXS, for example. Or you could > calculate the SAXS curve and get a better understanding of size and shape > differences between your protein and the reference, but that's more > advanced stuff. > > J > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsur...@gmail.com> > wrote: > > > Also you must know, a lot analysis are available over the entire manual > of > > Gromacs where all cannot be performed. Gromacs always provide you all > > necessary analysis but to choose which one is always your choice that > suits > > your simulation purpose. > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysic...@gmail.com> > > wrote: > > > > > Hi, > > > > > > > > > Thank you for your prompt reply. > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > "over particular PC sub space" > > > > > > Could you please elaborate a bit? > > > > > > Thanks a lot once again. > > > > > > Thanks, > > > Neha > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <drrahulsur...@gmail.com > > > > > wrote: > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysic...@gmail.com > > > > > > wrote: > > > > > > > > > Hi gromacs users, > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > > protein > > > > > folding? > > > > > > > > > > How to do it? > > > > > > > > > > I want to ascertain if there is any conformation change in protein > > > where > > > > > the ligand binds. Is it possible? > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want > to > > > > make > > > > > observation through MD simulation which is not obtained through > > > docking. > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > > measure > > > > the structural changes. > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > Thanks, > > > > > Neha > > > > > -- > > > > > 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. > > > > > > > -- > > > 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. > > > -- > 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.
