THanks. I have one more system dioxin + water molecules. There is possiblity of C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water. I want to calculate the number of hydrogen bonds. I used the following command g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num I selected the hydrogen atom and oxygen atom of water
Igot this error Checking for overlap in atoms between H96 and O21 Calculating hydrogen bonds between H96 (4 atoms) and O21 (256 atoms) Found 0 donors and 256 acceptors No Donors found ------------------------------------------------------- Program g_hbond, VERSION 4.0.5 Source code file: gmx_hbond.c, line: 2235 Fatal error: Nothing to be done Nilesh On Mon, August 30, 2010 10:47 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> I have a system with a glucose molecule and 256 water molecules. >> I want to find out the number of hydrogen bond between the hydrogen atom >> of OH group of glucose and the oxygen atom of water. How can I make >> the index file. > > Type "help" at the make_ndx prompt for examples. These groups are very > easy to create by specifying the desired atom names. > > -Justin > > >> Thanks >> >> >> 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/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/mailing_lists/users.php > > > -- 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/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/mailing_lists/users.php
