On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul <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>> 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/> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> >> http://www.bevanlab.biochem.__**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> >> > >> >> ==============================**__========== >> -- gmx-users mailing list 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> >> > >> 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>> >> 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>>. >> >> >> 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> >> > >> >> >> 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. > > ==============================**========== > > 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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