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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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