On 3/14/18 11:57 PM, Dilip H N wrote:
1) I tried with the Nitrogen atom of glycine and the oxygen atom of water also using the command gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg but still, i am getting the same error as:- Specify 2 groups to analyze: Group 0 ( N) has 1 elements Group 1 ( OW) has 511 elements Select a group: 0 Selected 0: 'N' Select a group: 1 Selected 1: 'OW' Checking for overlap in atoms between N and OW Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms) Found 0 donors and 512 acceptors No Donors found ------------------------------------------------------- Program: gmx hbond, version 2016.2 Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732) Fatal error: Nothing to be done 2) I tried to find out the distance between Calpha(Ca) and Ow from the command gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg but still, i am getting the same error as above one. Any suggestions...
Neither of your groups has any H atoms. gmx hbond can't calculate hydrogen bonds without them.
-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.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
