[gmx-users] tpr without top-file
zoon at science.uva.nl
Fri Oct 1 12:07:55 CEST 2004
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.
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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