On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <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 | (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> > 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? Steven
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