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

[MD]

I know what you mean, but I didn't see any other molecules getting too
close to the ring :)

On Wed, Jan 17, 2018 at 6:11 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you poke your finger into something, it isn't going to stay flat. :-)
>
> Mark
>
> On Wed, Jan 17, 2018 at 9:44 PM MD <refmac5 at gmail.com> wrote:
>
> > Hi Mark,
> > Can you tell me more details about the ring's atoms interacting with an
> > environment? What interactions did you mean?
> > Thanks,
> > Ming
> >
> > 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?
> > >
> > > 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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