Generate missing atoms of a coarse grained structure

From: Mert Gür (
Date: Sun Apr 04 2010 - 04:40:13 CDT

Dear all,
I have predicted a structure of a protein using a coarse grained
model. i.e. I only have the Carbon Alpha coordinates.
I also have the pdb file of this protein for a different structure.

What I want to do, is to find the closest realistic structure (with
all its atoms) to the predicted structure.
For that purpose I have to first generate the missing atoms of the
predicted coarse grained structure .
Then perform an additional short minimization.

I was planning to use TMD for that purpose. Starting with the
structure provided in the pdb file I will force the carbon alpha atoms
to go
to the predicted coordinates and the minimize it.

Do you have better suggestions how to generate the missing atoms of
the predicted structure .Also any comments/critics on using TMD for
this purpose will be of big help.

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