One question.... for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain. How about other amino acids and their maximum hbonds they can create?
Steven On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you for clarification Justin!!! The Manual is not as clear as you :P > > Steven > > On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul <jalem...@vt.edu>wrote: > >> >> >> Steven Neumann wrote: >> >>> >>> >>> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >>> jalem...@vt.edu>> wrote: >>> >>> >>> >>> Steven Neumann wrote: >>> >>> >>> >>> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul >>> <jalem...@vt.edu <mailto:jalem...@vt.edu> >>> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >>> >>> >>> >>> Steven Neumann wrote: >>> >>> Hi Gromacs Users, >>> I have calculated hydrogen bonds and collisions between my >>> ligands and every single residue using g_hbond. Looking >>> at the >>> criteria adpoted by Gromacs I found impossible that number >>> of >>> hydrogen bonds were higher than number of collisions... >>> And what >>> is interesting in one of my residue I obtained result like >>> this... All Hbonds with Glycine - 1872, All Collisions 704. >>> Does anyone know how is it possible? >>> >>> I don't know how any of your numbers are possible (1872 H-bonds >>> forming with a glycine?), or what you are defining as a >>> collision >>> and how you calculated it. Please provide the exact commands >>> that >>> you're using. If you're equating a contact (e.g. from >>> g_mindist) >>> with a collision, then realize that the default criteria for a >>> contact are very different than the geometric criteria for a >>> hydrogen bond. >>> >>> -Justin >>> >>> -- ==============================**____========== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540) >>> >>> 231-9080 <tel:%28540%29%20231-9080> >>> <tel:%28540%29%20231-9080> >>> >>> http://www.bevanlab.biochem. >>> <http://www.bevanlab.biochem./**>____vt.edu/Pages/Personal/** >>> justin <http://vt.edu/Pages/Personal/justin> >>> >>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>> >>> >>> >>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >> >>> >>> ==============================**____========== >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>**> >>> >>> >>> >>> >>> http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users> >>> >>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> > >>> >>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> <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> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> > >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> >>> <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 >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> > >>> <mailto:gmx-users-request@__gr**omacs.org<http://gromacs.org/> >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >>. >>> >>> Can't post? Read >>> >>> http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> > >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >>> >>> >>> My system is made of 10 ligands and one protein. I used command: >>> g_hbond -f md.trr -s md.tpr -n res91.ndx -num >>> 91with10LIGbonds.xvg >>> Where I specified in the index file two groups: 10 ligands and >>> Glycine residue. So I have calculated hbonds (second column) and >>> collisions (third column) and then I made a sum of all frames >>> during 100 ns simualtion time (one frame every 50 ps) obtaining >>> 1872 hbonds and 703 collisions between Glycine and 10 ligands. I >>> did it with every residue to assess binding affinity of >>> different amino acids. >>> Criteria for collision is distance <3.5 A, and fo hbond distance >>> <3.5 A and angle. So when calcualting hbond and collisions the >>> number of hbonds has has to be smaller while collision takes >>> into account hbonds as welll. I obtained results like this for >>> all other residues which seems to be correct. Am I right? >>> >>> No. The second column is not inclusive of the first. It counts the >>> number of atoms that are within hydrogen bonding distance, but do >>> not meet the criteria because of the angle between D-H-A. >>> >>> >>> -Justin >>> >>> In this case number of collisions has to include number of hbonds. >>> If collision is counted as a distance <3.5 and hbond distance <3.5 >>> plus angle D-H-A means that collisions covers hbonds... Explain >>> please whether I am wrong. >>> >>> >> The second column lists the number of atom pairs that satisfy the distance >> requirement but do not satisfy the angle requirement and therefore are not >> hydrogen bonds. The two columns are mutually exclusive. The sum of these >> two columns would be the total number of pairs that are within >> hydrogen-bonding distance, but the first column indicates those that are >> actually involved in hydrogen bonds (because of the angle), and the second >> column indicates those that are not involved in hydrogen bonds. >> >> >> -Justin >> >> -- >> ==============================**========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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 list gmx-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> >> > >
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