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

[Mark Abraham]

Hi,

You still have many sources of problems (e.g. the warnings you suppressed,
the fact that your ring's atoms interact with an environment). What happens
when you minimize a capped peptide in vacuo?

Mark

On Tue, Jan 16, 2018 at 12:39 PM MD <refmac5 at gmail.com> wrote:

> Hi Justin,
>
> I got the itp and parameters of my side chain modified amino acid from
> CHARMM-GUI and incorporated it into my protein structure, labeled with
> HETATM. I made the atom types names consistent with charmm forcefield which
> I used with gromacs and made sure overall the parameters look decent for
> now. After some fixing the grompp would run with no warnings, and I did a
> quick energy minimization, but ended up with a distorted six member ring. I
> have the picture and my parameters attached. Your time is appreciated :)
>
>
> https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-rgIesxy0QdIHm7tqTug/edit?usp=sharing
>
> Ming
>
> On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
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