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.
---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
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Received on Tue Nov 13 2012 - 06:00:04 PST
