[gmx-users] analyzing amber trajectories with gromacs

Marie-Pierre Durrieu Marie-Pierre.Durrieu at ibpc.fr
Mon Mar 14 19:09:44 CET 2005


I've converted Amber trajectories into xtc in order to use the Gromacs 
analysis tools. Some of these tools require a tpr, so I need to create a 
topology file. Is there an easy way to do it ? The problem is that using 
a Gromacs force field like OPLS changes the order of atoms.

I've thought about 3 possibilities :

-changing the order of atoms in the residue database ; but how will the 
topology file be affected ?
-using x2top
-using a conversion script like ambconv

By the way, why does g_helix need a tpr ? Why is the trajectory plus 
structure not sufficient to compute the helix properties ?

Thanks in advance for your response,


Marie-Pierre Durrieu
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75 005 Paris - FRANCE
e-mail : marie-pierre.durrieu at ibpc.fr
Tel: +33 15841 5161

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