[gmx-users] Re: g_hbond
magiofer at gmail.com
Tue Jan 17 14:08:23 CET 2006
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
On 1/17/06, Kia Balali-Mood <kia.balali-mood at bioch.ox.ac.uk> wrote:
> Hi MG,
> Yes ..there is something missing!
> You need to create a specific index file (type "make_ndx -h" into your
> 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
> > Message: 3
> > Date: Tue, 17 Jan 2006 11:45:35 +0100
> > From: MGi? <magiofer at gmail.com>
> > Subject: [gmx-users] g_hbond
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> > <e6acc8ab0601170245x7375a4bah65b7147fff37f393 at mail.gmail.com>
> > 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
> > 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
> > 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)
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