[gmx-users] hbond analysis

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Thu Oct 30 12:58:12 CET 2014

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
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

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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