Thanks, Kia,<br>
actually I have used an index.ndx file, but the output is the same.
I'll try anyway with the automated procedure by the shell script. Thank
you anyway<br>
Maria Giovanna<br><br><div><span class="gmail_quote">On 1/17/06, <b class="gmail_sendername">Kia Balali-Mood</b> <<a href="mailto:kia.balali-mood@bioch.ox.ac.uk">kia.balali-mood@bioch.ox.ac.uk</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi MG,<br><br>Yes ..there is something missing!<br>You need to create a specific index file (type "make_ndx -h" into your command<br>line for details!) having separate groupings of the protein and ligand. you<br>
then put this index file into g_hbond.<br><br>To automate this you can type ...<br>echo X X | g_hbond -f traj.trr -s topol.tpr -n index.ndx -g hbond.log -num<br>-dist -ang -hbn<br><br>whereby X is the index file no. of your ligand and protein
<br><br>perhaps creating a shell script will be of use if u r doing this with a lot of<br>complexes. though you need to change the name of the output files<br><br>Hope this helps<br><br>Kia<br><br><br>> Message: 3<br>> Date: Tue, 17 Jan 2006 11:45:35 +0100
<br>> From: MGi? <<a href="mailto:magiofer@gmail.com">magiofer@gmail.com</a>><br>> Subject: [gmx-users] g_hbond<br>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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<br>><br>> Hi users!<br>> I'm trying and obtain the hydrogen bonds of a protein to a ligand or vice<br>> versa. I get the number of hbonds forming during the course of the<br>> trajectory (hbnum.xvg), the name of the donors and acceptors, but my
<br>> hbond.log file is always empty and so it is also the [hbonds_protein-ligand]<br>> section of the hbond.ndx file. My command line was:<br>><br>> g_hbond -f traj.trr -s topol.tpr -g -num -dist -ang -hbn<br>
><br>> is anything missing?<br>> thanks for any help,<br>> yours,<br>> MG<br>><br><br>--<br>Kia Balali-Mood PhD, CBiol, MIBiol<br>Postdoctoral Research Associate, Department of Biochemistry,<br>Oxford University, OX1 3QU, UK
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