[gmx-users] Contraints on both angles and dihedrals

[Ahmet Yildirim]

Hi,

The flexibility of the ligand due to its internal motions is a big issue
when I turn off protein-ligand interactions in the decoupled state (state
1). Applying Boresch's restraints between the protein and ligand, applying
positional retraints on all the atoms of the ligand or adding dihedral
restraints is not sufficient to get the rigidified ligand in the case that
the ligand is very flexible.  So, if the ligand were quite rigid, the
target system (state 1) would be sufficiently similar to the reference
system (state 0). For instance, the intersection of the work distributions
of the forward (0-->1) and backward (1-->0) state would provide the
accurate estimates of free energy...
If GROMACS have the ability to constraint all the internal coordinates of
the ligand, then the cost of the angle, bond and dihedral constraints can
be calculated with an extra step. That is easy.

Do you have any plans for the implementation of such a feature to the next
version of GROMACS-2018.1? :)




On 9 May 2018 at 11:36, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Of what would that be a good physical model?
>
> Mark
>
> On Wed, May 9, 2018, 10:07 Ahmet Yildirim <ahmedo047 at gmail.com> wrote:
>
> > Hi,
> >
> > With stiff restraints using standard GROMACS versions I couldn't get what
> > I want. If Developers implement some like this:
> > contraints-grps = ligand
> > constrains = all-bonds all-angles all-dihedrals
> >
> > it would be wonderful :)
> >
> > > On 9 May 2018, at 10:56, Felipe Merino <
> > felipe.merino at mpi-dortmund.mpg.de> wrote:
> > >
> > > Hi,
> > >
> > > I guess you can always get a similar final result using some stiff
> > restraints with gromacs/plumed.
> > >
> > > Best
> > >
> > > Felipe
> > >
> > >
> > >> On 09/05/18 09:48, Ahmet Yildirim wrote:
> > >> Hi,
> > >>
> > >> I am facing with the same problem... Unfortunately GROMACS does not
> have
> > >> the capability to constraint all the internal coordinates (bond
> lengths,
> > >> bond angles and dihedral angles) of a certain group (e.g. ligand) in
> the
> > >> simulation system. Hope that Developers will take into consideration
> the
> > >> implementation of such a feature to the next version :)
> > >>
> > >>
> > >>
> > >>> On 8 May 2018 at 14:23, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > >>>
> > >>> Hi,
> > >>>
> > >>> There is no general support for rigid body dynamics in GROMACS.
> > >>>
> > >>> Mark
> > >>>
> > >>>> On Tue, May 8, 2018, 12:52 Qasim Pars <qasimpars at gmail.com> wrote:
> > >>>>
> > >>>> Dear users,
> > >>>>
> > >>>> I would like to constraint all the angles and dihedrals of a ligand
> to
> > >>>> make it rigid but Gromacs does not have this capability for the
> > >>> dihedrals.
> > >>>> However, the angle and dihedral restraints do not make it rigid as I
> > >>> want,
> > >>>> as it is very flexible.
> > >>>>
> > >>>> Do you have an idea on how I can make the ligand rigid using
> gromacs?
> > >>>>
> > >>>> Thanks in advance,
> > >>>> --
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> > >>>>
> > >>> --
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> > >>
> > >>
> > >
> > > --
> > > Felipe Merino,
> > > Max Planck Institute for Molecular Physiology
> > > Department of Structural Biochemistry
> > > Otto-Hahn-Str. 11
> > > 44227 Dortmund
> > > Phone: +49 231 133 2307
> > >
> > > ORCID:  https://orcid.org/0000-0003-4166-8747
> > > Publons: https://publons.com/a/1305699/
> > > Researchgate: https://www.researchgate.net/profile/Felipe_Merino
> > >
> > > --
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-- 
Ahmet Yildirim