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
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Received on Wed Jan 16 2013 - 10:00:03 PST
