Re: High RMSD of Coarse grain Protein

From: Hannes Loeffler (
Date: Mon Oct 18 2010 - 09:01:20 CDT

On Mon, 18 Oct 2010 17:22:18 +0530
sunita gupta <> wrote:

> 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?

Maybe your coarse-grained model (you didn't tell us which one) cannot
reliably reproduce your protein's structure? Some of those models need
to operate with additional restraints like "elastic bonds" to keep up
the structure. Backtransformation will, naturally, always lead to a
loss in information and there is no unique way to do so.

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