[MMTK] Visualize a trajectory

Matteo Memelli ryu-jin@bigfoot.com
Thu, 19 Apr 2001 13:33:45 CEST


(...)
> What am I missing?

>>A database entry for the ligand. Which is rather easy to write if
>>you have the force field parameters for the ligand, but these
>>may not be so easy to find.

>>Konrad.

First of all thank you very much for your advice, and sorry for the dumb
question, but I'm a student at the beginning  in Molecular Modelling.
I wrote an entry for my ligand (benzo(a)pyrene) in the Database, running
some trajectories and everything is ok :)
Anyway I'm trying to visualize a trajectory with VMD (following your
suggestion) but when I try to export a dcd file from the "nc" trajectory
using dcd_trajectory.py or to visualize it directly using
view_trajectory.py I get this error:

bash-2.03$ python dcd_export.py 
Traceback (most recent call last):
  File "dcd_export.py", line 16, in ?
    trajectory = Trajectory(None, "dna_bap.nc")
  File "/usr/local/lib/python2.0/site-packages/MMTK/Trajectory.py", line
100, in __init__
    universe = skeleton.make(conf)
  File "/usr/local/lib/python2.0/site-packages/MMTK/Skeleton.py", line 111,
in make
    collection.addObject(o.make(conf))
  File "/usr/local/lib/python2.0/site-packages/MMTK/Skeleton.py", line 93,
in make
    self.kwargs)
  File "/usr/local/lib/python2.0/site-packages/MMTK/NucleicAcids.py", line
165, in __init__
    sequence = map(Biopolymers._fullName, sequence)
  File "/usr/local/lib/python2.0/site-packages/MMTK/Biopolymers.py", line
116, in _fullName
    return _residue_names[string.lower(residue)]
KeyError: dc5

Note that I'm still using the DNA strand from MMTK and that I changed the
name 'bala.nc' to my new traj. name in the dcd_trajectory.py file.Dumping a
text file from the trajectory one using "ncdump" I can see a
'dc5dgdgdcdcdg3\' entry in the description entry. Still missing something!

thx
Matte

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