Dear Justin I think I have confused so much. Let me try to put it in simple way.
1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? 2. Time step of monomer(just protein) simulation is 150ns and protein-ligand complex is 50ns. In this case is it valid to compare the above analyses between monomer and complex? Dear Justin I apologise if I am not to your mark to explain in better way. On Wed, 7 Jun 2017 at 1:19 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/6/17 1:11 PM, RAHUL SURESH wrote: > > Dear Justin > > > > Thank you. I am considering Rmsd rmsf rg as just supplementary analysis > > for my study. My aim to analyse conformational change in protein. I > would > > like to bring a note on protein stability after ligand binding. I don't > > know to which part of monomer I can compare the rmsd of complex with. > > First 50ns or last .. can you please help me with this? > > I'm not following. You're talking about monomers and time intervals as if > they're interchangeable. What's the story? Do you have a multimer? Are > you > curious about demonstrating convergence? > > -Justin > > > On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> On 6/6/17 2:12 AM, RAHUL SURESH wrote: > >>> Dear Users > >>> > >>> *Exp procedure:* > >>> I have simulated the protein monomer for 150ns. Using the 150ns > >> conformer, > >>> ligand is docked to the protein using autodock and the simulation is > >>> carried out for 50ns. > >>> > >>> *Analysis:* > >>> > >>> Is it possible to compare my RMSD, RMSF, ROG analysis of complex system > >>> with that of monomer? If yes which part of the monomer trajectory > should > >> be > >>> considered.? > >>> > >> > >> This is up to you to determine in light of whatever your goals are in > >> running > >> the simulation. What are you trying to test or determine? Unless the > >> protein's > >> stability is seriously impacted by the ligand, RMSD and Rg are useless. > >> RMSF > >> might be useful if there are motions that are amplified or damped by > ligand > >> binding. Run the analysis and see what happens on a per-residue basis. > >> > >> -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. > >> > > -- > ================================================== > > 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. > -- *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.
