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
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Received on Tue Nov 13 2012 - 02:30:02 PST
