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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