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? 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 > > > 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. > > 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.