[gmx-users] water mediated hydrogen bond
Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned objective. But I'm not sure how to use it Can any one help me with what data I should have before running the script and how I can get such a data and also how shuld I use the data as a input for the script?. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/water-mediated-hydrogen-bond-tp5003358.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] water mediated hydrogen bond
On 11/29/12 10:18 AM, Raj wrote: Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned objective. But I'm not sure how to use it Can any one help me with what data I should have before running the script and how I can get such a data and also how shuld I use the data as a input for the script?. Thanks in advance My script will tell you how long a particular hydrogen bond persists, in terms of the percentage of time occupied in a given trajectory. Likely what I suggested was to use the same logic to parse an hbmap.xpm file to determine when hydrogen bonds existed simultaneously between different proteins and a common water molecule. One could, in theory, expand the script I wrote to do this. Having never had a need to make such modifications, I cannot provide much more insight, but I know it is possible. -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 -- 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] water mediated hydrogen bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] water mediated hydrogen bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] water Mediated Hydrogen Bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
