Hi,
Amber trajectory formats store box information as vectors using 6
coordinates (3 lengths and 3 angles) only. It sounds like your box
coordinates may not have been written at all. If you open your
trajectory in cpptraj with the following input:
parm <your parm file>
trajin <your amber traj file> 1 1
go
You should see output like:
INPUT TRAJECTORIES:
[<your amber traj>] is an AMBER trajectory, Parm 0 (with box info)
(reading 1 of 10)
If it doesn't say "(with box info)" then for some reason your box
coordinates didn't get translated between the formats. What is the
exact procedure you are using in VMD to save your coordinates (are you
saving as 'crdbox'?).
-Dan
PS - There will be direct support for reading gromacs trajectories in
the next release of AmberTools.
On Wed, Jan 16, 2013 at 7:04 AM, Federica Chiappori
<federica.chiappori.itb.cnr.it> wrote:
> Dear all,
> I'm trying to convert a gromacs trajectory (xtc) in an amber trajectory
> (mdcrd) to apply the MMPBSA tool, I obtain the mdcrd with vmd, wile
> MMPBSA.py returns:
> "error in box coord line of trajectory
> expected only 3 or 6 box coords"
>
> Box of the gromacs trajectory is a dodecahedron, so I have 9 box coords,
> can vmd write the correct box coords?
> How can I convert the box coords for amber?
>
> Thanks,
> Best regards.
> Federica
>
> --
> _____________________________________________________________
> Federica Chiappori, Ph.D.
> Istituto di Tecnologie Biomediche - CNR
> Via F.lli Cervi, 93
> 20090 Segrate (MI)
> Phone: +39 02 26422606
> E-mail: federica.chiappori.itb.cnr.it
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jan 16 2013 - 08:00:03 PST
