Dear gromacs users, I am having some problems with hbond analysis using gromacs. I am interested in hbonds between certain amino acids for example: LYS256 and nucleic acid that has number 2 in my files. I generated the index file which contains r256 and r2 by running make_ndx -f gro -o out.ndx then I run g_hbond g_hbond -f traj.xtc -s .tpr -num hydrogen-bonds-protein.xvg
My xvg file did not contain any hbond between those amino acids, which is not true. I do not know what went wrong. Could anyone suggest me something? Is there any other way to run the hbond? Is it possible to use the xtc trajectory and run hbond anlysis in ptraj? or can I convert it somehow? Best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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.
