[gmx-users] tpr without top-file

Peter Zoon zoon at science.uva.nl
Fri Oct 1 12:07:55 CEST 2004

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.

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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