Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will obviously not sit in the binding site....
Dr. Vitaly V. Chaban On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil <divyasunilku...@gmail.com>wrote: > 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
