no. what you are looking for is a side chain optimization program. This is
global optimization. Amber will do local optimization. Perhaps others on
this list will know of good ways to find the best side chain rotamers.
On Wed, Jun 15, 2011 at 10:26 AM, abc def <biotechabc.gmail.com> wrote:
> 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 - 08:00:04 PDT
