[gmx-users] tpr without top-file
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 1 13:46:19 CEST 2004
On Fri, 2004-10-01 at 12:07, Peter Zoon wrote:
> Hi all,
> Here's the story. We wrote a program which converts trajectories from
> Macromodel to xtc. We obtain a initial gro file and the trajectory in
> xtc format. We would like to use the gromacs analysis routines to
> analyze the trajectory. We a looking at a rotaxane in particular we want
> to study the hydrogen bonds between the macrocycle and the thread and
> the dihedrals within the thread.
the problem I presume it the topology. How about generating one using
prodrg? Many analysis tools can substitute the tpr file for a gro/pdb
file but g_hbond needs the atom names and the connectivity.
g_dih actually also needs the topology, although some things can be done
with just an index file (g_angle, which also analyses dihedrals)
> G_hbond needs a tpr file, but since we have no topology (and cannot
> create one easily) its a problem to get a tpr. Is there anyway around this?
> Could I for instance write a "fake" topology which only has the
> connectivities, the atom-types and masses and somehow create a tpr file
> from only this information and than run the analysis?
> Any other suggestions would also be greatly appreciated.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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