It is said that the crystallographic B-factor measures both the
thermal fluctuation (including conformational heterogeneity of
proteins) and global translation and rotation. In our calculation
B-factors, however, the global translation/rotation has been removed
by rigid-body alignment. Therefore, one might expect that the
calculated B-factors should be smaller than the experimental ones.
But the calculated B-factors I have obtained are larger than the
experimental ones. Here in my bfactor.in file.
Bfactor.in:
trajin 1npt.mdcrd
reference min.pdb
center :1-373 origin mass
image origin center familiar
rms reference out protein.out :1-372.CA
rms reference out ligand.out :373
atomicfluct out bfactor.out .CA byatom bfactor
Is that anything wrong with my bfactor.in? thank you for your suggestion!
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Received on Sun Aug 07 2005 - 16:53:00 PDT
