[gmx-users] analyzing amber trajectories with gromacs

[Marie-Pierre Durrieu]

Hi,

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.


-- 
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