[MMTK] converting Amber trajectories

Randy M. Wadkins rwadkin@jhmi.edu
Tue, 25 Jun 2002 12:33:45 -0400


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