Thanks Mark, Depends what you mean by "stability." Actually, I don't know the role of metal ion if it is used as co-factor by a particular protein. I thought to do comparative analysis by MD simulation which might predict the possible role of metal (in this case Zn^2+). Other analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have already done, but I want to get insight in their energetic terms while addressing the question why such changes occurred? According to the best of my study, there is no experimental data available for my target protein and that's why I want to predict its free-energy of folding or whatever else. Will you kindly suggest me some hand notes or tutorial like to do free-energy analysis for both the systems; means a) protein with metal ion and b) protein without metal ion?
Amir On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Depends what you mean by "stability." A well designed study could seek to > measure or estimate the difference in the free-energy of folding, but that > would probably require an infeasibly large amount of sampling, and be > highly dependent on the quality of the parameterization of the > metal-protein interactions, for which you would probably need some suitable > experimental data. > > Mark > > On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb <zebami...@gmail.com> wrote: > > > Hi gromacs users, > > > > I want to calculate the energy for comparative analysis of protein with > and > > without metal ion, wherein I would like to determine the influence of > metal > > on protein structural stability. I have used gromacs for simulation. > Please > > suggest me how to do this kind of analysis? Should i follow a specific > > tutorial? > > > > Amir > > -- > > 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.