I defined donor and hydrogen both in donor group. Acceptors are in acceptor group.
Nilesh ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Tuesday, April 10, 2018 6:45:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] GMX hbond On 4/10/18 6:43 PM, Dhumal, Nilesh wrote: > I tried, didn't find the proper answer. I run the simulation using Gromacs > 4.5 version and used g_hbond successfully. Could not find out why its not > working using gmx hbond. No version of GROMACS should have ever worked with such index groups. A hydrogen bond must be defined by at least three atoms, because it is based on both the D-A distance and the D-H-A angle. One cannot do the analysis on a group that contains only H atoms. Your donors have to include both D and H atoms, and the acceptor group the A atoms. -Justin > Nilesh > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul <jalem...@vt.edu> > Sent: Tuesday, April 10, 2018 6:39:37 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] GMX hbond > > > > On 4/10/18 5:51 PM, Dhumal, Nilesh wrote: >> Hello Gromacs users, >> >> >> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION >> 5.1.4. I did following steps >> >> mx hbond -f traj.trr -s md.tpr -n index.ndx -ac >> >> Reading file md.tpr, VERSION 5.1.4 (single precision) >> Specify 2 groups to analyze: >> Group 0 ( System) has 2560 elements >> Group 1 ( Other) has 2432 elements >> Group 2 ( EMI) has 2432 elements >> Group 3 ( CL) has 128 elements >> Group 4 ( Ion) has 128 elements >> Group 5 ( EMI) has 2432 elements >> Group 6 ( CL) has 128 elements >> Group 7 ( C) has 128 elements >> Group 8 ( C2) has 128 elements >> Group 9 ( C4) has 128 elements >> Group 10 ( H9) has 128 elements >> Group 11 ( H10) has 128 elements >> Group 12 ( H11) has 128 elements >> Group 13 ( CL) has 128 elements >> Group 14 ( ch) has 256 elements >> Group 15 ( ch) has 3 elements >> Group 16 ( O1) has 2 elements >> Select a group: 14 >> Selected 14: 'ch' >> Select a group: 13 >> Selected 13: 'CL' >> Checking for overlap in atoms between ch and CL >> Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms) >> Found 0 donors and 0 acceptors >> Making hbmap structure...done. >> No Donors or Acceptors found >> >> ------------------------------------------------------- >> Program gmx hbond, VERSION 5.1.4 >> Source code file: >> /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l >> >> ine: 3984 >> >> Fatal error: >> Nothing to be done >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> >> Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group >> is list of acceptors . Why donors and acceptors are zero. > Have you tried Googling the error? The first result has the answer... > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
