Sorry I was not aware of this command ... I couldn't find it in the
manual either (I hope I did not overlooked it) ..
Does it have the same synthax as "image"
Best,
Vlad
On 11/13/2012 03:00 PM, Jason Swails wrote:
> On Tue, Nov 13, 2012 at 8:53 AM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>> I patched AMBER 12 up to bugfix 26 (I have seen some bugfixes for
>> cpptraj, so I double check that they are applied).
>> I get my trajectories imaged correctly with ptraj as long as I fix
>> alpha, beta, gamma to 109.xxx ... degrees.
>>
>> In cpptraj I always get the error when using exactly the same "image
>> familiar" command as in ptraj (using "box alpha 109 beta 109 gamma 109
>> fixalpha fixbeta fixgamma" beforehand does not lead to correct imaging
>> as it happens in ptraj.
>>
> What happens if you use the "autoimage" command?
>
>
>> ---error message ---
>> Too many iterations in routine JACOBI
>> convergence failed
>>
>> Best,
>> Vlad
>>
>>
>>
>> On 11/13/2012 02:36 PM, Jason Swails wrote:
>>> What is the result of:
>>>
>>> cd $AMBERHOME && ./patch_amber.py --patch-level
>>>
>>> ?
>>>
>>> On Tue, Nov 13, 2012 at 5:00 AM, Vlad Cojocaru <
>>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>
>>>> Dear AMBER users,
>>>>
>>>> I generated trajectories with namd using a leap-generated topology with
>>>> a truncated octahedron box. I used the "wrap" command in namd.
>>>> Now I am trying to image these trajectories using cpptraj (AMBER 12). A
>>>> while ago I described a solution for this problem for ptraj (see thread
>>>> below). However this does not work in cpptraj ... The same commands
>>>> described in this thread give me either a "segmentation fault" or errors
>>>> such as "convergence failed" during imaging. It is also not exactly a
>>>> correct solution as the box changes during the simulations, so therefore
>>>> fixing it to a certain value is actually incorrect.
>>>>
>>>> Here is the thread I mentioned:
>>>> http://archive.ambermd.org/200908/0157.html
>>>>
>>>> Obviously the problem is that neither ptraj nor cpptraj are able to
>>>> properly read the box information from the DCD trajectories. I would
>>>> like to ask if anybody has any idea or interest to get cpptraj to
>>>> correctly process the DCD trajectories.
>>>>
>>>> Best wishes
>>>> Vlad
>>>>
>>>> --
>>>> Dr. Vlad Cojocaru
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Department of Cell and Developmental Biology
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Nov 13 2012 - 06:30:03 PST
