[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 12:27:04 CET 2013

On 1/17/13 6:22 AM, Anna Marabotti wrote:
> Dear all,
> we'd need to convert a trajectory in .xtc format (and the related topology file)
> to a format that could be read by Amber program (I'd need to perform MM-PBSA
> calculations).
> We tried to do it using VMD, but failed to produce a correct trajectory to be
> read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6
> box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9
> box coords.
> I read the gmx-user archive to find hints to overcome the problem, but only
> found incomplete, and in some cases quite old, suggestions (We are currently
> using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how
> to proceed, and I have even the doubt that this is not possible to do.
> Could you please give me some information about, possibly with detailed
> descriptions about the commands and the flags to use?

You can write a new box using trjconv and make it whatever you want.  Presumably 
you're stripping out water and such anyway, so all you would have to do is 
center your solute in whatever box you want:

trjconv -s topol.tpr -f traj.xtc -center -box x y z



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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