[MMTK] converting Amber trajectories

[Randy M. Wadkins]

Has anyone been able to convert Amber mdcrd trajectory files into 
something that the MMTK DCDReader can handle?  Using ptraj in the 
Amber7 distribution, I've converted the mdcrd file into a "charmm 
binary trajectory" file.  From ptraj:

OUTPUT COORDINATE FILE
   File (dyn3.dcd) is a CHARMM trajectory in little endian binary format

(I've also tried it with big endian format).

the DCDReader complains:

Traceback (most recent call last):
   File "analysis2.py", line 27, in ?
     dcd_reader()
   File "/usr/local/lib/python2.2/site-packages/MMTK/DCD.py", line 63, 
in __call__
     self.getActions(), self.getOption('dcd_file'))
ValueError: number of atoms in DCD file (673976) doesn't match universe (3170)

I don't know where MMTK is getting the 673976 value for number of 
atoms in the file, so I assume that this "charmm binary format" is 
not a DCD file.  Does anyone know of a utility to convert Amber 
trajectories into the proper format for MMTK?

Thanks.
--Randy