Indeed.
So, go to your main topology file and define a new atom type "Xe" under an appropriate section. Then just add sigma and epsilon in the non-bonded section and you are ready to explore the binding. Dr. Vitaly V. Chaban On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil <divyasunilku...@gmail.com>wrote: > ya.. but there is experimental data to confirm the presence. can you help > me to solve this problem > > > On 9 July 2013 11:54, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > >> 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 >> > > > > -- > "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
