[MMTK] c-alpha configuration form Amber force field

Ramon Crehuet rcrehuet at gmail.com
Tue May 19 14:39:03 UTC 2009


Dear MMTK users,
I would like to perform (iteratively) a c-alpha normal mode calculation from
an all-atom conformation and then apply the modes to this all-atom
conformation.
I though of having two universes, one with the Amber force field and another
with the C-alpha.
How can I copy the configuration in the amber universe to the c-alpha? I
have tried the following:

# Construct all atom system
universe = InfiniteUniverse(Amber94ForceField(.8,1.2))
universe.protein = Protein('a.pdb')

# Construct the associated c-alpha system
universe_ca = InfiniteUniverse(CalphaForceField())
universe_ca.protein = copy(universe.protein)

But then all atoms are copied to the c-alpha model. (and the normal mode
calculation seems to take all atoms because it collapses my computer
memory).
Which is the proper way to proceed?
Thanks,
Ramon
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