[gmx-users] MD of native complex

Justin Lemkul 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list