Re: [gmx-users] Xe atom
ok thank you very much. i will try and get back to u regards divya On 11 July 2013 14:26, Dr. Vitaly Chaban 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 >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 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 >> >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 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 > 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Xe atom
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 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 >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 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 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Xe atom
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 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 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 listgmx-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 listgmx-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
[gmx-users] MD with Xenon
hello, I have a protein in which I fixed Xenon in the binding sites. without xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which forcefield am I able to use? thanking you regards Divya -- gmx-users mailing listgmx-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
Re: [gmx-users] Number of atoms is very high
yes.. I tried both Dodecahedral and octahedral. But in both boxes, the long tail of the protein was outside. Only in cubic, the whole protein is inside. that's why I used that. On 27 February 2013 09:53, Tsjerk Wassenaar wrote: > As Justin hints, using a rhombic dodecahedron would bring the total > number of atoms under 1 lakh. > > :) > > Cheers, > > Tsjerk > > > On Tue, Feb 26, 2013 at 11:50 PM, Divya Sunil > wrote: > > Hello > > > > I have a protein consists of 2303 atoms. I simulated it in water using > > cubic box. As the protein has a long tail, the no. of water molecules to > > fill the box is very high (132235). After simulation I converted the .gro > > file to .pdb and in which I have seen that the atom number after 1 lakh > is > > again started to denote as 1 and also the molecule number after as > 1. > > So in this system there are 4 molecules that have number 1. Is this > create > > any problem during simulation/ before simulation? ( I noted this only > after > > simulation and the system was not hanged) Also is it possible to remove > > some water molecules manually after adding solvation to reduce the number > > of atoms? > > > > thanks and regards > > > > Divya > > -- > > gmx-users mailing listgmx-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 > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > gmx-users mailing listgmx-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." ## Divya G Nair Senior Research Fellow Bioinformatics Infrastructure Facility Dept:of Biotechnology and Microbiology Kannur University Kannur,Kerala,India-670 661 Phone: +91 9495112169 ## -- gmx-users mailing listgmx-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
Re: [gmx-users] Number of atoms is very high
ok..thank you very much On 26 February 2013 23:54, Justin Lemkul wrote: > > > On 2/26/13 5:50 PM, Divya Sunil wrote: > >> Hello >> >> I have a protein consists of 2303 atoms. I simulated it in water using >> cubic box. As the protein has a long tail, the no. of water molecules to >> fill the box is very high (132235). After simulation I converted the .gro >> file to .pdb and in which I have seen that the atom number after 1 lakh is >> again started to denote as 1 and also the molecule number after as 1. >> So in this system there are 4 molecules that have number 1. Is this create >> any problem during simulation/ before simulation? ( I noted this only >> after >> simulation and the system was not hanged) Also is it possible to remove >> some water molecules manually after adding solvation to reduce the number >> of atoms? >> >> > There is no problem during the simulation, and the fact that atom > numbering starts over is simply a limit of PDB format. Proper > representations can probably be obtained using other file formats. > Theoretically, there may be issues with creating index groups, but likely > only if dealing with water, and these issues can again likely be overcome > by choosing a different file format. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- "A man is great by deeds, not by birth." ## Divya G Nair Senior Research Fellow Bioinformatics Infrastructure Facility Dept:of Biotechnology and Microbiology Kannur University Kannur,Kerala,India-670 661 Phone: +91 9495112169 ## -- gmx-users mailing listgmx-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
