[gmx-users] Aromatic rings not plane after minimization

[Pierre THEVENET]

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?

Thank you.

--------------------------

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