High RMSD of Coarse grain Protein

From: sunita gupta (sunita.bio_at_gmail.com)
Date: Mon Oct 18 2010 - 06:52:18 CDT

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Hello all

I did coarse grain simulation of protein (92 residues), the RMSD of the
protein is in the range of 1.5 till a small restraints is on the protein
beads and as i remove all the restraints (in production).the RMSD shoots up
to 6.5 Armstrong . Also I am not able to get back the all-atom structure
from coarse grain trajectory , as the secondary structure is completely
lost.
Can any one help me with this sudden rise in RMSD and how to reverse bank
the coarse grain data to all-atom pdb?

Thanks in Advance

-- 
-- 
SUNITA GUPTA

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