Hi MG, Yes ..there is something missing! You need to create a specific index file (type "make_ndx -h" into your command line for details!) having separate groupings of the protein and ligand. you then put this index file into g_hbond. To automate this you can type ... echo X X | g_hbond -f traj.trr -s topol.tpr -n index.ndx -g hbond.log -num -dist -ang -hbn whereby X is the index file no. of your ligand and protein perhaps creating a shell script will be of use if u r doing this with a lot of complexes. though you need to change the name of the output files Hope this helps Kia > Message: 3 > Date: Tue, 17 Jan 2006 11:45:35 +0100 > From: MGi? > Subject: [gmx-users] g_hbond > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi users! > I'm trying and obtain the hydrogen bonds of a protein to a ligand or vice > versa. I get the number of hbonds forming during the course of the > trajectory (hbnum.xvg), the name of the donors and acceptors, but my > hbond.log file is always empty and so it is also the [hbonds_protein-ligand] > section of the hbond.ndx file. My command line was: > > g_hbond -f traj.trr -s topol.tpr -g -num -dist -ang -hbn > > is anything missing? > thanks for any help, > yours, > MG > -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)