[gmx-users] MD of native complex
jalemkul at vt.edu
Sun Sep 10 17:30:47 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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