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
>
--
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 - 06:30:02 PST
