[gmx-users] Aromatic rings not plane after minimization

[Mark Abraham]

On Apr 15, 2014 10:43 AM, "Pierre THEVENET" <pithevenet at free.fr> wrote:
>
> Hello everyone,
>
> I am using gromacs to perform a small minimization of the structure of my
> peptides, and some have aromatics rings (in tyrosines for example) .
Before
> the minimization the ring is perfectly plane (CB-CG and CZ-OH bonds are in
> the same plane than the aromatic ring).

Yes, probably by construction.

> However, after the minimization,
> the angle is different and I don't understand why. I tried different
> gromacs versions (
> 4.6.3 and 3.3.3), also different force fields included with gromacs, and I
> always have the loss of the perfect plane angle.

Nature doesn't have a ruler, though. Stuff will deviate from local ideal
behavior if there's something more pressing (literally). So the real
question is whether the deviations mean the model is suitable, or not.

> The atom typing is correct, I tried to see if options in my mdp file could
> be the cause of this issue but I couldn't find any option that could be
> responsible for such trouble.
>
> Can someone help me?

Planarity is encouraged by improper dihedral angles, but if they are
absent, or not strong enough in the face of other problems, planarity will
not be the result.

Mark

> Thank you.
>
> --------------------------
>
> Pierre THEVENET
> Ph.D. Student
> INSERM - MTi
> Ecole Doctorale B3MI
> Université Paris Diderot - Paris 7
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