I tried to use contact and -da together with following command g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc -noda -r 0.5 -contact -num
I am getting following error. Fatal error:Can not analyze contact between H and A: turn off -noda Nilesh On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote: > 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 [email protected] >>>> 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 [email protected]. 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 >> [email protected] http://folding.bmc.uu.se/ >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. Can't post? >> Read >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
