Hi,
'autoimage' is used by itself and replaces any 'center'/'image'
command combos. However I don't think this will help in your case. In
the AT12 version of cpptraj, unlike ptraj, the 'box' command will
modify topology box information but the angles are still read in from
the input trajectory (not fixed). However, it could be that something
else is happening here. Could you send me (again off-list) the
topology and 1 or 2 frames of your trajectory so I can track down
exactly what is happening here? Thanks.
-Dan
On Tue, Nov 13, 2012 at 7:11 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> 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
>
>
> _______________________________________________
> 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 Tue Nov 13 2012 - 07:30:03 PST
