[gmx-users] secondary structure element constraining

[Justin Lemkul]

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

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

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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