Unfortunately Chimera doesn't support the prmtop/DCD combo. The only possibility I can find is to convert your prmtop to a psf in VMD as described in this mail (option "a"):

But at that point you are already using VMD and I don't see why you wouldn't just go ahead and visualize your trajectory using that instead of relying on the shaky prmtop->psf conversion.

I will open a feature-request ticket in our Trac database for allowing "mix and match" of topology/coordinate formats, with you on the recipient list.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On Mar 2, 2010, at 3:43 AM, Francesco Musiani wrote:

Hi all,
I would like to visualize in Chimera a trajectory obtained with the program NAMD,
but I have a .prmtop topology file generated using AMBER instead of a .psf topology file.

I have these files beacuse in NAMD is possible to use AMBER format topology.

Is it possible to implement an additional feature in Chimera which allows to visualize
NAMD trajectory using AMBER topology?

Thanks in advance,

Francesco