[gmx-users] Aromatic rings not plane after minimization

[Dr. Vitaly Chaban]

On Tue, Apr 15, 2014 at 10:39 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). 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.
>
> 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?


Aromatic rings are literally delighted to deform, unless improper
dihedrals are defined in the topology.

I do not know how you do the magic connected with the topology
derivation, but please make sure that all needed dihedrals were
introduced. x2top, for instance, does not write dihedrals.

It is very unlikely that the MDP options can play any role in this problem.



Dr. Vitaly V. Chaban



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