[Chimera-users] NAMD trajectory and AMBER topology
pett at cgl.ucsf.edu
Tue Mar 2 14:28:25 PST 2010
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.
UCSF Computer Graphics Lab
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
> Is it possible to implement an additional feature in Chimera which
> allows to visualize
> NAMD trajectory using AMBER topology?
> Thanks in advance,
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