[gmx-users] Monitoring of Salt bridges during simulation Run
Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- 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] Monitoring of Salt bridges during simulation Run
You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html On Thu, Apr 5, 2012 at 5:23 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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] Monitoring of Salt bridges during simulation Run
g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Monitoring of Salt bridges during simulation Run
Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ? Also what is the real *-t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well? James * 5 апреля 2012 г. 12:36 пользователь Peter C. Lai p...@uab.edu написал: g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 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] Monitoring of Salt bridges during simulation Run
On 05/04/12, James Starlight jmsstarli...@gmail.com wrote: Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ? Use trjconv -n and tpbconv -n to create a matching subset of your trajectory and -s input file, and use that as input to g_saltbr. Also what is the real -t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well? Looks like Rmax to me, from g_saltbr -h, but if you experiment, find out and report back it can go into the next version of the documentation (which is never perfect!). Mark James 5 апреля 2012 г. 12:36 пользователь Peter C. Lai p...@uab.edu написал: g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 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
