[gmx-users] MD of native complex

[Justin Lemkul]

On 9/9/17 10:59 PM, Deep kumar wrote:
> Hello All,
> 
> I have done MD of a native pdb structure 2LL7 for 10ns. Looking at the
> trajectories in PyMOL, I see that in the native structure one of the helix
> (short separate chain ID) tends to unfold. Is this possible in the
> simulation of native complexes?
> 

Possible, yes, but likely, no.  Visualization software guesses what secondary 
structure should be based on assumptions of ideal geometries.  Often they get it 
wrong.  A conclusive analysis is done by DSSP, phi/psi dihedral measurements, etc.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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