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

[Mark Abraham]

Hi,

Sorry, I can't remember what you've said your workflows may once have
been...

Mark

On Sat, Jan 20, 2018, 13:46 MD <refmac5 at gmail.com> wrote:

> 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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