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

[MD]

On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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?
>

​Hi Mark, I minimized in vacuo condition and it ran but gave back similar
conformations. I looked back to see the warnings I suppressed you mentioned
previously and I am still confused what warnings you meant?

Thanks,

Ming​

>
> 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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