On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> 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? >> >> > > Any OH or NH group is a donor, any lone pair is an acceptor (though > obviously not modeled explicitly in MD). The ability of MD force fields to > agree with reality in this respect is debatable, but should come close. > > -Justin > > Thank you Justin. Can you please clarify me something and tell me whether I > am wrong. This is what I obtained from calulating hbonds between 10 ligands > and Glycine. Each ligand serve 8 OH group (flavanoid) : *Reading file md.tpr, VERSION 4.5.4 (single precision) Specify 2 groups to analyze: Group 0 ( r_96) has 7 elements -* this is my Glycine - 7 atoms (side chain - Hydrogen) *Group 1 ( LIG) has 510 elements -* these are 10 ligands, 51 atoms each, 8 OH group *Select a group: 0 1 Selected 0: 'r_96' Select a group: Selected 1: 'LIG' Checking for overlap in atoms between r_96 and LIG Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms) Found 81 donors and 112 acceptors * ** *81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I right?* *112 acceptors? 7 atoms of my Glycine x 12 possibilities?* ** *trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 11x11x11 grid, rcut=0.35 Last frame 2000 time 100000.000 Average number of hbonds per timeframe 0.642 out of 4536 possible - that is understood = (112x81)/2* ** *So how many possibilities has Glycine in order to create hbond? Shall I choose just a side chain which is hydrogen?* ** *Steven* > Steven >> >> >> On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann >> <s.neuman...@gmail.com<mailto: >> 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 >> <mailto: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> >> <mailto: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>> >> <mailto: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/> <http://vt.edu/> | (540) >> >> 231-9080 <tel:%28540%29%20231-9080> >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem >> <http://www.bevanlab.biochem/>**. >> >> >> <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://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. >> <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>**> >> <mailto: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> >> >> >> <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> >> >> >> <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> >> >> >> <mailto:gmx-users-request@ >> >> <mailto:gmx-users-request@>__g**r__omacs.org<http://gr__omacs.org/>< >> http://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> >> >> >> >> <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 <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> >> > >> >> >> >> > -- > ==============================**========== > > 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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