[gmx-users] six member ring won't stay flat

[Justin Lemkul]

On 1/15/18 7:45 PM, MD wrote:
> Hi Gromacs,
>
> I have a modified side chain amino acid and it has a six member ring
> attached to it. Regarding this ring I had dihedral angles taken care with
> some 0s and some 180s. However, after minimization my structure looks very
> strange, the ring is not flat and the dihedral angles in my settings didn't
> seem to apply to the minimized structure at all. Any thoughts?

You're going to have to provide a lot more detail. You're parametrizing 
something nonstandard, so there are plenty of places to make mistakes. 
Without knowing your structure, the actual parameters and how derived 
and validated them, there's nothing to do but guess.

Keep in mind that rings are not necessarily perfectly planar, and the 
values set for dihedral phase offsets do not strictly mean the values 
that the dihedrals must adopt.

-Justin

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

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