Ya basically I want to sample different rotamers for finding the best
suitable one for docking purpose. So for that what I need to generate
different rotamers. Will the NMR restraint work for it?
Thanks
Pooja Khurana
On Wed, Jun 15, 2011 at 7:46 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> are you trying to sample different rotamers in your minimization? or are
> you
> trying to restrain to the initial rotamer? If you want to restrain them,
> you
> can do this using the NMR restraints. There are many examples in the
> archives. The data is specified in the disang file.
>
> On Wed, Jun 15, 2011 at 10:11 AM, abc def <biotechabc.gmail.com> wrote:
>
> > Hi,
> >
> > I have gone through the basic ones. By rotatable bonds I mean that
> > supposedly in a molecule / protein ligand a C is connected to four
> > different
> > heavy atoms and that may be connected further to any atoms either by
> > single/double/triple bond. So the bond say C-C is single..and hence can
> be
> > easily rotated unmlike the bond say C=O. So I want to restrict the
> > minimization of all those bonds involving C in sp3 hybridized form, for
> > example.
> >
> > Similarly there may be more such bonds in the ligand molecule. How can
> this
> > be done? Or can you please direct me to the tutorial in which such a
> > minimization has been employed?
> >
> > Thanks,
> >
> > Pooja Khurana
> >
> > On Wed, Jun 15, 2011 at 4:02 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > what exactly do you mean by minimization of the rotatable bonds?
> > > have you worked through the tutorials on the amber web site?
> > > On Wed, Jun 15, 2011 at 6:01 AM, Pooja Khurana <btpooja.yahoo.in>
> wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > Is it possible to do the restraint minimization of the rotatable
> bonds
> > in
> > > a
> > > > molecule?
> > > > And if yes then how it can be done? Actually I am a beginner, so need
> > > some
> > > > help to implement the same.
> > > >
> > > > Hoping for an early reply.
> > > >
> > > > Thanks in anticipation,
> > > >
> > > > Pooja Khurana
> > > > B.E. Biotechnology
> > > > India
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Received on Wed Jun 15 2011 - 07:30:07 PDT
