Hello, You may follow " http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ " Everything will go fine
Good luck Amir On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. <adarsh_p13008...@nitc.ac.in> wrote: > Dear all, > > We have a 419 amino acid long protein and planned Protein-ligand complex MD > simulation using Gromacs 5.1.4 to check. > > 1. What sought of MD simulation we have to perform?. > 2. Restrain protein alone or Restrain both protein and ligand during > simulation?. > 3. What is the exact command for Drug positional RMSD plot? > 4. What is the exact command for Number of Hydrogen bond plot? > 5. What is the exact command for Other interactions between protein and > ligand? > 6. how to view the trajectory files? or We have to convert the frames to > *.pdb and view in Pymol? > > Regards, > Adarsh V. K. > -- > 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.
