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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 16 2013 - 10:30:02 PST
