Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms.
Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: > Try the -contact option. > > > Erik > > > > Nilesh Dhumal skrev 2011-04-11 17.12: > >> Is there any way to specify clorin and florin atoms as a receptor. >> >> >> Nilesh >> >> >> On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: >> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> I am trying to calculate number of hydrogen bond (O-H---CL)in my >>>> system. >>>> >>>> I use the following command >>>> >>>> >>>> >>>> >>>> g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num >>>> >>>> >>>> Output file hbnum.xvg shows zero number of hydorgen bond. >>>> >>>> >>>> >>>> Can you tell me why its showing zero no. >>>> >>>> >>>> >>>> A strong peak is found in rdf between H and CL at 2.0 A. >>>> >>>> >>>> >>> Chlorine is not considered a receptor in g_hbond. >>> >>> >>> >>> -Justin >>> >>> >>> >>>> I am using Gromacs 4.0.7 version. >>>> >>>> >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> >>> >>> 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 >>> >>> >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> 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 >>> >>> >>> >>> >> > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://folding.bmc.uu.se/ > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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