[gmx-users] six member ring won't stay flat
jalemkul at vt.edu
Tue Jan 16 01:53:34 CET 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users