thanks for the reply.. I am planning to place Xe in the protein binding site ( just like a metal atom). I made a topology file with xe charge and mass. I have two options to implement the simulation. 1. like protein-ligand simulation. 2. replacing a number of solvent (water) molecules with xe in the cubic system. for these purposes what is the correct procedure?... do I need to simply add the xe parameters to .gro file and topol file? or may i need to make changes in forcefield? pls help
Thanking you Divya On 8 July 2013 19:16, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > I am a too curious person not to ask WHY Xe is of interest in connection > with the protein..? > > > Dr. Vitaly V. Chaban > > > On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 7/8/13 9:21 AM, divyasunil wrote: > > > >> Hello, > >> > >> Please help me to add Xe atom to GROMOS96 53a6 force field. I need to > >> carry > >> out a protein-Xe simulation . I tried myself but failed. > >> > >> > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- "A man is great by deeds, not by birth." ################################## Dr. Divya G. Nair Post Doctoral Fellow Institute of Biophysics and Physical Biochemistry University of Regensburg Regensburg-93040 Germany ################################## -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists