>>> Box of the gromacs trajectory is a dodecahedron, so I have 9 box coords,
I don't believe AMBER programs support that.
Bill
Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Does the topology file you are using match your trajectory? Was your
> trajectory stripped in any way? This problem can also occur if the #
> of atoms in your topology is greater than the # of atoms in the
> trajectory.
>
> -Dan
>
> On Wed, Jan 16, 2013 at 10:52 AM, Federica Chiappori
> <federica.chiappori.itb.cnr.it> wrote:
> > Dear Dan,
> > thank you for your reply.
> > cpptraj returns the same result as MMPBSA.py:
> > Error in box coord line of trajecory
> > Expect only 3 or 6 box coords
> > Problem with line: (line after box coords)
> >
> > To convert the trajectory I simply saved as crdbox in vmd.
> >
> > Federica
> >
> > Il 16/01/2013 16:45, Daniel Roe ha scritto:
> >> 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
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> > --
> > _____________________________________________________________
> > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > 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 - 15:30:04 PST
