[MMTK] Using MMTK

Matias Saavedra 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
Amber94ForceField ?

Is the RigidMotionSubspace detailed enough to consider
all the interactions forces in the protein for the
calculations?


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.

Matias Saavedra


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