[MMTK] Using MMTK
matias_saavedra at yahoo.com
Mon Jul 18 16:50:15 CEST 2005
Hi, i'm using MMTK to determine the flexibility in the
active site of some proteins.
The calculation time for minimization and Normal Mode
analysis is too long on a 300 aa protein (in my
personal powerbook G4). So i switched to subspaces.
With RigidMotionSubspace my computer take 3 hours to
calculate the Normal Modes of my 300 aa protein. Is
there a way to reduce the calculation time, but
keeping all the detailed analysis given by
Is the RigidMotionSubspace detailed enough to consider
all the interactions forces in the protein for the
In the other hand, it is posible to realize a
minimization in MMTK and obtain the newly generated
structure conformation ? (this is to perform just one
minimization in a structure, and be able to save the
minimized structure in order to use it later without
the need of minimizing again).
Thanks a lot for your concern.
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