[gmx-users] secondary structure element constraining

Justin Lemkul jalemkul at vt.edu
Mon Jun 11 14:08:34 CEST 2018

On 6/10/18 3:04 AM, alex rayevsky wrote:
> Dear users!
> Did anybody meet the problem of positional constraints applied to the
> secondary structure, namely keeping the 310-helix stable all the time? I've
> modelled the substructure - a bundle of alpha helices with a 310 helix
> segment (longer, thinner, reactive) on the one of them. And I need to hold
> this conformation intact, to study other rearrangements. I'm not sure that
> freezing is a good way to nail 3-5 residues in a huge system, maybe it is
> somehow robust. At the same time I tried to simulate the helix with
> restraints (10000 kJ/A^2 XYZ per each atom of the 310 helix part) and the
> helix moved to the low energy state with a transition '310 -> alpha
> conformation' without any obstacles. Usually I'm using COM pulling code,
> but I don't know how to put some constraint on the backbone of these
> several residues (forming triangle instead of the square, while looking
> through the helix) without any relation to a surrounding system (without
> reference atoms), just like a freezing but more realistic, allowing some
> harmonic oscillations. Any suggestions??

It sounds like you want dihedral restraints on your phi and psi torsions.



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


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