ok thank you very much. i will try and get back to u regards divya
On 11 July 2013 14:26, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > 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 > -- "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
