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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 13 2012 - 06:00:03 PST
