[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.
> cheers
> Peter
> >  
> >
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list